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Chang LY, Lee MZ, Wu Y, Lee WK, Ma CL, Chang JM, Chen CW, Huang TC, Lee CH, Lee JC, Tseng YY, Lin CY. Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles. Nucleic Acids Res 2024; 52:e17. [PMID: 38096046 PMCID: PMC10853793 DOI: 10.1093/nar/gkad1187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 02/10/2024] Open
Abstract
Pathway analysis, including nontopology-based (non-TB) and topology-based (TB) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. By considering dependencies and interactions between genes, TB methods usually perform better than non-TB methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most TB methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge.
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Affiliation(s)
- Lan-Yun Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Meng-Zhan Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Yujia Wu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Kai Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chia-Liang Ma
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Jun-Mao Chang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Ciao-Wen Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Tzu-Chun Huang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chia-Hwa Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, New Taipei City 235, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, New Taipei City 235, Taiwan
| | - Jih-Chin Lee
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 110, Taiwan
| | - Yu-Yao Tseng
- Department of Food Science, Nutrition, and Nutraceutical Biotechnology, Shih Chien University, Taipei 104, Taiwan
| | - Chun-Yu Lin
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
- Institute of Data Science and Engineering, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- School of Dentistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Luo H, Lao L, Au KS, Northrup H, He X, Forget D, Gauthier MS, Coulombe B, Bourdeau I, Shi W, Gagliardi L, Fragoso MCBV, Peng J, Wu J. ARMC5 controls the degradation of most Pol II subunits, and ARMC5 mutation increases neural tube defect risks in mice and humans. Genome Biol 2024; 25:19. [PMID: 38225631 PMCID: PMC10789052 DOI: 10.1186/s13059-023-03147-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Neural tube defects (NTDs) are caused by genetic and environmental factors. ARMC5 is part of a novel ubiquitin ligase specific for POLR2A, the largest subunit of RNA polymerase II (Pol II). RESULTS We find that ARMC5 knockout mice have increased incidence of NTDs, such as spina bifida and exencephaly. Surprisingly, the absence of ARMC5 causes the accumulation of not only POLR2A but also most of the other 11 Pol II subunits, indicating that the degradation of the whole Pol II complex is compromised. The enlarged Pol II pool does not lead to generalized Pol II stalling or a generalized decrease in mRNA transcription. In neural progenitor cells, ARMC5 knockout only dysregulates 106 genes, some of which are known to be involved in neural tube development. FOLH1, critical in folate uptake and hence neural tube development, is downregulated in the knockout intestine. We also identify nine deleterious mutations in the ARMC5 gene in 511 patients with myelomeningocele, a severe form of spina bifida. These mutations impair the interaction between ARMC5 and Pol II and reduce Pol II ubiquitination. CONCLUSIONS Mutations in ARMC5 increase the risk of NTDs in mice and humans. ARMC5 is part of an E3 controlling the degradation of all 12 subunits of Pol II under physiological conditions. The Pol II pool size might have effects on NTD pathogenesis, and some of the effects might be via the downregulation of FOLH1. Additional mechanistic work is needed to establish the causal effect of the findings on NTD pathogenesis.
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Affiliation(s)
- Hongyu Luo
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.
| | - Linjiang Lao
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Xiao He
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Diane Forget
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Marie-Soleil Gauthier
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada
| | - Isabelle Bourdeau
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
- Division of Endocrinology, CHUM, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Wei Shi
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Lucia Gagliardi
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, Australia
- Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, Australia
- Endocrine and Diabetes Unit, Queen Elizabeth Hospital, Adelaide, Australia
| | - Maria Candida Barisson Villares Fragoso
- Unidade de Suprarrenal Disciplina de Endocrinologia E Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Junzheng Peng
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada
| | - Jiangping Wu
- Centre de Recherche, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, QC, Canada.
- Department of Medicine, Université de Montréal, Montreal, QC, Canada.
- Division of Nephrology, CHUM, Montreal, QC, Canada.
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3
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Rios F, Uriostegui-Arcos M, Zurita M. Transcriptional Stress Induces the Generation of DoGs in Cancer Cells. Noncoding RNA 2024; 10:5. [PMID: 38250805 PMCID: PMC10801504 DOI: 10.3390/ncrna10010005] [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: 11/21/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
A characteristic of the cellular response to stress is the production of RNAs generated from a readthrough transcription of genes, called downstream-of-gene-(DoG)-containing transcripts. Additionally, transcription inhibitor drugs are candidates for fighting cancer. In this work, we report the results of a bioinformatic analysis showing that one of the responses to transcription inhibition is the generation of DoGs in cancer cells. Although some genes that form DoGs were shared between the two cancer lines, there did not appear to be a functional correlation between them. However, our findings show that DoGs are generated as part of the cellular response to transcription inhibition like other types of cellular stress, suggesting that they may be part of the defense against transcriptional stress.
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Affiliation(s)
| | | | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca Morelos 62250, Mexico (M.U.-A.)
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4
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Li XL, Xie Y, Chen YL, Zhang ZM, Tao YF, Li G, Wu D, Wang HR, Zhuo R, Pan JJ, Yu JJ, Jia SQ, Zhang Z, Feng CX, Wang JW, Fang F, Qian GH, Lu J, Hu SY, Li ZH, Pan J. The RNA polymerase II subunit B (RPB2) functions as a growth regulator in human glioblastoma. Biochem Biophys Res Commun 2023; 674:170-182. [PMID: 37423037 DOI: 10.1016/j.bbrc.2023.06.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/11/2023]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive brain tumor with a poor prognosis. The growth of GBM cells depends on the core transcriptional apparatus, thus rendering RNA polymerase (RNA pol) complex as a candidate therapeutic target. The RNA pol II subunit B (POLR2B) gene encodes the second largest subunit of the RNA pol II (RPB2); however, its genomic status and function in GBM remain unclear. Certain GBM data sets in cBioPortal were used for investigating the genomic status and expression of POLR2B in GBM. The function of RPB2 was analyzed following knockdown of POLR2B expression by shRNA in GBM cells. The cell counting kit-8 assay and PI staining were used for cell proliferation and cell cycle analysis. A xenograft mouse model was established to analyze the function of RPB2 in vivo. RNA sequencing was performed to analyze the RPB2-regulated genes. GO and GSEA analyses were applied to investigate the RPB2-regulated gene function and associated pathways. In the present study, the genomic alteration and overexpression of the POLR2B gene was described in glioblastoma. The data indicated that knockdown of POLR2B expression suppressed tumor cell growth of glioblastoma in vitro and in vivo. The analysis further demonstrated the identification of the RPB2-regulated gene sets and highlighted the DNA damage-inducible transcript 4 gene as the downstream target of the POLR2B gene. The present study provides evidence indicating that RPB2 functions as a growth regulator in glioblastoma and could be used as a potential therapeutic target for the treatment of this disease.
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Affiliation(s)
- Xiao-Lu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Yi Xie
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Yan-Ling Chen
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China; School of Basic Medicine and Biological Sciences, Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Zi-Mu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Yan-Fang Tao
- Department of Hematology, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Gen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Di Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Hai-Rong Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Ran Zhuo
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Jing-Jing Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Juan-Juan Yu
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Si-Qi Jia
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China; School of Basic Medicine and Biological Sciences, Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Zheng Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Chen-Xi Feng
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Jian-Wei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Guang-Hui Qian
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Shao-Yan Hu
- Department of Hematology, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Zhi-Heng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China; Department of Hematology, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
| | - Jian Pan
- Institute of Pediatric Research, Children's Hospital of Soochow University, Soochow, Jiangsu Province, 215003, China.
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5
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Liu X, Liu X, Du Y, Zou D, Tian C, Li Y, Lan X, David CJ, Sun Q, Chen M. Aberrant accumulation of Kras-dependent pervasive transcripts during tumor progression renders cancer cells dependent on PAF1 expression. Cell Rep 2023; 42:112979. [PMID: 37572321 DOI: 10.1016/j.celrep.2023.112979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/05/2023] [Accepted: 07/31/2023] [Indexed: 08/14/2023] Open
Abstract
KRAS is the most commonly mutated oncogene in human cancer, and mutant KRAS is responsible for over 90% of pancreatic ductal adenocarcinoma (PDAC), the most lethal cancer. Here, we show that RNA polymerase II-associated factor 1 complex (PAF1C) is specifically required for survival of PDAC but not normal adult pancreatic cells. We show that PAF1C maintains cancer cell genomic stability by restraining overaccumulation of enhancer RNAs (eRNAs) and promoter upstream transcripts (PROMPTs) driven by mutant Kras. Loss of PAF1C leads to cancer-specific lengthening and accumulation of pervasive transcripts on chromatin and concomitant aberrant R-loop formation and DNA damage, which, in turn, trigger cell death. We go on to demonstrate that the global transcriptional hyperactivation driven by Kras signaling during tumorigenesis underlies the specific demand for PAF1C by cancer cells. Our work provides insights into how enhancer transcription hyperactivation causes general transcription factor addiction during tumorigenesis.
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Affiliation(s)
- Xinhong Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiangzheng Liu
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yingxue Du
- Tsinghua University School of Life Sciences, Beijing 100084, China
| | - Di Zou
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Chen Tian
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yong Li
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xun Lan
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Charles J David
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Qianwen Sun
- Tsinghua University School of Life Sciences, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Mo Chen
- State Key Laboratory of Molecular Oncology, SXMU-Tsinghua Collaborative Innovation Center for Frontier Medicine, School of Medicine, Tsinghua University, Beijing 100084, China.
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6
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Gaggioli V, Lo CSY, Reverón-Gómez N, Jasencakova Z, Domenech H, Nguyen H, Sidoli S, Tvardovskiy A, Uruci S, Slotman JA, Chai Y, Gonçalves JGSCS, Manolika EM, Jensen ON, Wheeler D, Sridharan S, Chakrabarty S, Demmers J, Kanaar R, Groth A, Taneja N. Dynamic de novo heterochromatin assembly and disassembly at replication forks ensures fork stability. Nat Cell Biol 2023; 25:1017-1032. [PMID: 37414849 PMCID: PMC10344782 DOI: 10.1038/s41556-023-01167-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/16/2023] [Indexed: 07/08/2023]
Abstract
Chromatin is dynamically reorganized when DNA replication forks are challenged. However, the process of epigenetic reorganization and its implication for fork stability is poorly understood. Here we discover a checkpoint-regulated cascade of chromatin signalling that activates the histone methyltransferase EHMT2/G9a to catalyse heterochromatin assembly at stressed replication forks. Using biochemical and single molecule chromatin fibre approaches, we show that G9a together with SUV39h1 induces chromatin compaction by accumulating the repressive modifications, H3K9me1/me2/me3, in the vicinity of stressed replication forks. This closed conformation is also favoured by the G9a-dependent exclusion of the H3K9-demethylase JMJD1A/KDM3A, which facilitates heterochromatin disassembly upon fork restart. Untimely heterochromatin disassembly from stressed forks by KDM3A enables PRIMPOL access, triggering single-stranded DNA gap formation and sensitizing cells towards chemotherapeutic drugs. These findings may help in explaining chemotherapy resistance and poor prognosis observed in patients with cancer displaying elevated levels of G9a/H3K9me3.
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Affiliation(s)
- Vincent Gaggioli
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Calvin S Y Lo
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zuzana Jasencakova
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Heura Domenech
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hong Nguyen
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Simone Sidoli
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrey Tvardovskiy
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Sidrit Uruci
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yi Chai
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | | | - Eleni Maria Manolika
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ole N Jensen
- Department of Biochemistry & Molecular Biology, VILLUM Centre for Bioanalytical Sciences and Centre for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sriram Sridharan
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Singapore
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Jeroen Demmers
- Proteomics Center and Department of Biochemistry, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus University Medical Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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7
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Dovrou A, Bei E, Sfakianakis S, Marias K, Papanikolaou N, Zervakis M. Synergies of Radiomics and Transcriptomics in Lung Cancer Diagnosis: A Pilot Study. Diagnostics (Basel) 2023; 13:738. [PMID: 36832225 PMCID: PMC9955510 DOI: 10.3390/diagnostics13040738] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Radiotranscriptomics is an emerging field that aims to investigate the relationships between the radiomic features extracted from medical images and gene expression profiles that contribute in the diagnosis, treatment planning, and prognosis of cancer. This study proposes a methodological framework for the investigation of these associations with application on non-small-cell lung cancer (NSCLC). Six publicly available NSCLC datasets with transcriptomics data were used to derive and validate a transcriptomic signature for its ability to differentiate between cancer and non-malignant lung tissue. A publicly available dataset of 24 NSCLC-diagnosed patients, with both transcriptomic and imaging data, was used for the joint radiotranscriptomic analysis. For each patient, 749 Computed Tomography (CT) radiomic features were extracted and the corresponding transcriptomics data were provided through DNA microarrays. The radiomic features were clustered using the iterative K-means algorithm resulting in 77 homogeneous clusters, represented by meta-radiomic features. The most significant differentially expressed genes (DEGs) were selected by performing Significance Analysis of Microarrays (SAM) and 2-fold change. The interactions among the CT imaging features and the selected DEGs were investigated using SAM and a Spearman rank correlation test with a False Discovery Rate (FDR) of 5%, leading to the extraction of 73 DEGs significantly correlated with radiomic features. These genes were used to produce predictive models of the meta-radiomics features, defined as p-metaomics features, by performing Lasso regression. Of the 77 meta-radiomic features, 51 can be modeled in terms of the transcriptomic signature. These significant radiotranscriptomics relationships form a reliable basis to biologically justify the radiomics features extracted from anatomic imaging modalities. Thus, the biological value of these radiomic features was justified via enrichment analysis on their transcriptomics-based regression models, revealing closely associated biological processes and pathways. Overall, the proposed methodological framework provides joint radiotranscriptomics markers and models to support the connection and complementarities between the transcriptome and the phenotype in cancer, as demonstrated in the case of NSCLC.
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Affiliation(s)
- Aikaterini Dovrou
- Digital Image and Signal Processing Laboratory, School of Electrical and Computer Engineering (ECE), Technical University of Crete, GR-73100 Chania, Greece
| | - Ekaterini Bei
- Digital Image and Signal Processing Laboratory, School of Electrical and Computer Engineering (ECE), Technical University of Crete, GR-73100 Chania, Greece
| | - Stelios Sfakianakis
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, GR-70013 Heraklion, Greece
| | - Kostas Marias
- Computational BioMedicine Laboratory, Institute of Computer Science, Foundation for Research and Technology-Hellas, GR-70013 Heraklion, Greece
- Department of Electrical and Computer Engineering, Hellenic Mediterranean University, GR-71410 Heraklion, Greece
| | - Nickolas Papanikolaou
- Computational Clinical Imaging Group, Champalimaud Clinical Centre, Champalimaud Foundation, Avenida Brasilia, 1400-038 Lisbon, Portugal
| | - Michalis Zervakis
- Digital Image and Signal Processing Laboratory, School of Electrical and Computer Engineering (ECE), Technical University of Crete, GR-73100 Chania, Greece
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8
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Qin W, Li L, Yang F, Wang S, Yang GY. High-throughput iSpinach fluorescent aptamer-based real-time monitoring of in vitro transcription. BIORESOUR BIOPROCESS 2022; 9:112. [PMID: 38647769 PMCID: PMC10991154 DOI: 10.1186/s40643-022-00598-0] [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: 07/15/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
In vitro transcription (IVT) is an essential technique for RNA synthesis. Methods for the accurate and rapid screening of IVT conditions will facilitate RNA polymerase engineering, promoter optimization, and screening for new transcription inhibitor drugs. However, traditional polyacrylamide gel electrophoresis (PAGE) and high-performance liquid chromatography methods are labor intensive, time consuming and not compatible with real-time analysis. Here, we developed an inexpensive, high-throughput, and real-time detection method for the monitoring of in vitro RNA synthesis called iSpinach aptamer-based monitoring of Transcription Activity in Real-time (STAR). STAR has a detection speed at least 100 times faster than conventional PAGE method and provides comparable results in the analysis of in vitro RNA synthesis reactions. It also can be used as an easy and quantitative method to detect the catalytic activity of T7 RNA polymerase. To further demonstrate the utility of STAR, it was applied to optimize the initially transcribed region of the green fluorescent protein gene and the 3T4T variants demonstrated significantly enhanced transcription output, with at least 1.7-fold and 2.8-fold greater output than the wild-type DNA template and common transcription template, respectively. STAR may provide a valuable tool for many biotechnical applications related to the transcription process, which may pave the way for the development of better RNA-related enzymes and new drugs.
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Affiliation(s)
- Weitong Qin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liang Li
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Fan Yang
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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9
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Lao L, Bourdeau I, Gagliardi L, He X, Shi W, Hao B, Tan M, Hu Y, Peng J, Coulombe B, Torpy DJ, Scott HS, Lacroix A, Luo H, Wu J. ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia. Nucleic Acids Res 2022; 50:6343-6367. [PMID: 35687106 PMCID: PMC9226510 DOI: 10.1093/nar/gkac483] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 12/13/2022] Open
Abstract
ARMC5 is implicated in several pathological conditions, but its function remains unknown. We have previously identified CUL3 and RPB1 (the largest subunit of RNA polymerase II (Pol II) as potential ARMC5-interacting proteins. Here, we show that ARMC5, CUL3 and RBX1 form an active E3 ligase complex specific for RPB1. ARMC5, CUL3, and RBX1 formed an active E3 specific for RPB1. Armc5 deletion caused a significant reduction in RPB1 ubiquitination and an increase in an accumulation of RPB1, and hence an enlarged Pol II pool in normal tissues and organs. The compromised RPB1 degradation did not cause generalized Pol II stalling nor depressed transcription in the adrenal glands but did result in dysregulation of a subset of genes, with most upregulated. We found RPB1 to be highly expressed in the adrenal nodules from patients with primary bilateral macronodular adrenal hyperplasia (PBMAH) harboring germline ARMC5 mutations. Mutant ARMC5 had altered binding with RPB1. In summary, we discovered that wildtype ARMC5 was part of a novel RPB1-specific E3. ARMC5 mutations resulted in an enlarged Pol II pool, which dysregulated a subset of effector genes. Such an enlarged Pol II pool and gene dysregulation was correlated to adrenal hyperplasia in humans and KO mice.
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Affiliation(s)
- Linjiang Lao
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Isabelle Bourdeau
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Lucia Gagliardi
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Endocrine and Diabetes Unit, Queen Elizabeth Hospital, Adelaide, SA5011, Australia
| | - Xiao He
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Wei Shi
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Bingbing Hao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Minjia Tan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yan Hu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Junzheng Peng
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Benoit Coulombe
- Department of Translational Proteomics, Institut de Recherches Cliniques de Montréal, Montréal, Québec, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - David J Torpy
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA5000, Australia
| | - Hamish S Scott
- Adelaide Medical School, University of Adelaide, Adelaide, SA5000, Australia.,Department of Genetics and Molecular Pathology, SA Pathology, Adelaide, SA5006, Australia.,Centre for Cancer Biology, an alliance between SA Pathology and the University of South Australia, Adelaide, SA5001, Australia.,UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA5001, Australia
| | - Andre Lacroix
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Endocrinology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Hongyu Luo
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
| | - Jiangping Wu
- Centre de recherché, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada.,Nephrology Division, Centre hospitalier de l'Université de Montréal (CHUM), Montréal, Québec H2X 0A9, Canada
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10
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Merino C, Casado M, Piña B, Vinaixa M, Ramírez N. Toxicity of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) in early development: A wide-scope metabolomics assay in zebrafish embryos. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:127746. [PMID: 35086039 DOI: 10.1016/j.jhazmat.2021.127746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/29/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
The tobacco-specific nitrosamine 4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is a carcinogenic and ubiquitous environmental pollutant for which toxic activity has been thoroughly investigated in murine models and human tissues. However, its potential deleterious effects on vertebrate early development are yet poorly understood. In this work, we characterized the impact of NNK exposure during early developmental stages of zebrafish embryos, a known alternative model for mammalian toxicity studies. Embryos exposed to different NNK concentrations were monitored for lethality and for the appearance of malformations during the first five days after fertilization. LC-MS based untargeted metabolomics was subsequently performed for a wide-scope assay of NNK-related metabolic alterations. Our results revealed the presence of not only the parental compound, but also of two known NNK metabolites, 4-Hydroxy-4-(3-pyridyl)-butyric acid (HPBA) and 4-(Methylnitrosamino)-1-(3-pyridyl-N-oxide)-1-butanol (NNAL-N-oxide) in exposed embryos likely resulting from active CYP450-mediated α-hydroxylation and NNK detoxification pathways, respectively. This was paralleled by a disruption in purine and pyrimidine metabolisms and the activation of the base excision repair pathway. Our results confirm NNK as a harmful embryonic agent and demonstrate zebrafish embryos to be a suitable early development model to monitor NNK toxicity.
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Affiliation(s)
- Carla Merino
- Universitat Rovira i Virgili, Departament d'Enginyeria Electrònica, Elèctrica i Automàtica, Tarragona, Spain; Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Casado
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Benjamí Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research, Spanish Council for Scientific Research (IDAEA-CSIC), Barcelona, Spain
| | - Maria Vinaixa
- Universitat Rovira i Virgili, Departament d'Enginyeria Electrònica, Elèctrica i Automàtica, Tarragona, Spain; Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
| | - Noelia Ramírez
- Universitat Rovira i Virgili, Departament d'Enginyeria Electrònica, Elèctrica i Automàtica, Tarragona, Spain; Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
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11
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Jiang Q, Zhang J, Li F, Ma X, Wu F, Miao J, Li Q, Wang X, Sun R, Yang Y, Zhao L, Huang C. POLR2A Promotes the Proliferation of Gastric Cancer Cells by Advancing the Overall Cell Cycle Progression. Front Genet 2021; 12:688575. [PMID: 34899822 PMCID: PMC8655910 DOI: 10.3389/fgene.2021.688575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 11/01/2021] [Indexed: 12/24/2022] Open
Abstract
RNA polymerase II subunit A (POLR2A) is the largest subunit encoding RNA polymerase II and closely related to cancer progression. However, the biological role and underlying molecular mechanism of POLR2A in gastric cancer (GC) are still unclear. Our study demonstrated that POLR2A was highly expressed in GC tissue and promoted the proliferation of GC in vitro and in vivo. We also found that POLR2A participated in the transcriptional regulation of cyclins and cyclin-dependent kinases (CDKs) at each stage and promoted their expression, indicated POLR2A’s overall promotion of cell cycle progression. Moreover, POLR2A inhibited GC cell apoptosis and promoted GC cell migration. Our results indicate that POLR2A play an oncogene role in GC, which may be an important factor involved in the occurrence and development of GC.
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Affiliation(s)
- Qiuyu Jiang
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Jinyuan Zhang
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Fang Li
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Xiaoping Ma
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Fei Wu
- Department of Oncology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Jiyu Miao
- Department of Hematology, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Qian Li
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China
| | - Xiaofei Wang
- Biomedical Experiment Center, Xian Jiaotong University, Xi'an, China
| | - Ruifang Sun
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Yang Yang
- Department of Toxicology and Sanitary Analysis, School of Public Health, Xi'an Jiaotong University, Xi'an, China
| | - Lingyu Zhao
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
| | - Chen Huang
- Institute of Genetics and Development Biology, Translational Medcine Institute, Xi'an Jiaotong University, Xi'an, China
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12
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Out-of-distribution generalization from labelled and unlabelled gene expression data for drug response prediction. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00408-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Parrello D, Vlasenok M, Kranz L, Nechaev S. Targeting the Transcriptome Through Globally Acting Components. Front Genet 2021; 12:749850. [PMID: 34603400 PMCID: PMC8481634 DOI: 10.3389/fgene.2021.749850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
Transcription is a step in gene expression that defines the identity of cells and its dysregulation is associated with diseases. With advancing technologies revealing molecular underpinnings of the cell with ever-higher precision, our ability to view the transcriptomes may have surpassed our knowledge of the principles behind their organization. The human RNA polymerase II (Pol II) machinery comprises thousands of components that, in conjunction with epigenetic and other mechanisms, drive specialized programs of development, differentiation, and responses to the environment. Parts of these programs are repurposed in oncogenic transformation. Targeting of cancers is commonly done by inhibiting general or broadly acting components of the cellular machinery. The critical unanswered question is how globally acting or general factors exert cell type specific effects on transcription. One solution, which is discussed here, may be among the events that take place at genes during early Pol II transcription elongation. This essay turns the spotlight on the well-known phenomenon of promoter-proximal Pol II pausing as a step that separates signals that establish pausing genome-wide from those that release the paused Pol II into the gene. Concepts generated in this rapidly developing field will enhance our understanding of basic principles behind transcriptome organization and hopefully translate into better therapies at the bedside.
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Affiliation(s)
- Damien Parrello
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Maria Vlasenok
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lincoln Kranz
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
| | - Sergei Nechaev
- Department of Biomedical Sciences, University of North Dakota School of Medicine, Grand Forks, ND, United States
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14
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Cruz-Ruiz S, Urióstegui-Arcos M, Zurita M. The transcriptional stress response and its implications in cancer treatment. Biochim Biophys Acta Rev Cancer 2021; 1876:188620. [PMID: 34454982 DOI: 10.1016/j.bbcan.2021.188620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
Cancer cells require high levels of transcription to survive and maintain their cancerous phenotype. For several years, global transcription inhibitors have been used in the treatment of cancer. However, recent advances in understanding the functioning of the basal transcription machinery and the discovery of new drugs that affect the components of this machinery have generated a new boom in the use of this type of drugs to treat cancer. Inhibiting transcription at the global level in the cell generates a stress situation in which the cancer cell responds by overexpressing hundreds of genes in response to this transcriptional stress. Many of these over-transcribed genes encode factors that may be involved in the selection of cells resistant to the treatment and with a greater degree of malignancy. In this study, we reviewed various examples of substances that inhibit global transcription, as well as their targets, that have a high potential to be used against cancer. We also analysed what kinds of genes are overexpressed in the response to transcriptional stress by different substances and finally we discuss what types of studies are necessary to understand this type of stress response to have more tools to fight cancer.
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Affiliation(s)
- Samantha Cruz-Ruiz
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mor., Mexico
| | - Maritere Urióstegui-Arcos
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mor., Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210 Cuernavaca, Mor., Mexico.
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15
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Baker A, Khan MS, Iqbal MZ, Khan MS. Tumor-targeted Drug Delivery by Nanocomposites. Curr Drug Metab 2021; 21:599-613. [PMID: 32433002 DOI: 10.2174/1389200221666200520092333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/30/2020] [Accepted: 03/24/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Tumor-targeted delivery by nanoparticles is a great achievement towards the use of highly effective drug at very low doses. The conventional development of tumor-targeted delivery by nanoparticles is based on enhanced permeability and retention (EPR) effect and endocytosis based on receptor-mediated are very demanding due to the biological and natural complications of tumors as well as the restrictions on the design of the accurate nanoparticle delivery systems. METHODS Different tumor environment stimuli are responsible for triggered multistage drug delivery systems (MSDDS) for tumor therapy and imaging. Physicochemical properties, such as size, hydrophobicity and potential transform by MSDDS because of the physiological blood circulation different, intracellular tumor environment. This system accomplishes tumor penetration, cellular uptake improved, discharge of drugs on accurate time, and endosomal discharge. RESULTS Maximum drug delivery by MSDDS mechanism to target therapeutic cells and also tumor tissues and sub cellular organism. Poorly soluble compounds and bioavailability issues have been faced by pharmaceutical industries, which are resolved by nanoparticle formulation. CONCLUSION In our review, we illustrate different types of triggered moods and stimuli of the tumor environment, which help in smart multistage drug delivery systems by nanoparticles, basically a multi-stimuli sensitive delivery system, and elaborate their function, effects, and diagnosis.
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Affiliation(s)
- Abu Baker
- Nanomedicine & Nanobiotechnology Lab, Department of Biosciences, Integral University, Lucknow, 226026, India
| | - Mohd Salman Khan
- Clinical Biochemistry & Natural Product Research Lab, Department of Biosciences, Integral University, Lucknow, 226026, India
| | - Muhammad Zafar Iqbal
- Department of Studies and Research in Zoology, Government First Grade College, Karwar, 581301, India
| | - Mohd Sajid Khan
- Nanomedicine & Nanobiotechnology Lab, Department of Biosciences, Integral University, Lucknow, 226026, India
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16
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Berico P, Cigrang M, Davidson G, Braun C, Sandoz J, Legras S, Vokshi BH, Slovic N, Peyresaubes F, Gene Robles CM, Egly JM, Compe E, Davidson I, Coin F. CDK7 and MITF repress a transcription program involved in survival and drug tolerance in melanoma. EMBO Rep 2021; 22:e51683. [PMID: 34296805 DOI: 10.15252/embr.202051683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/09/2022] Open
Abstract
Melanoma cell phenotype switching between differentiated melanocytic and undifferentiated mesenchymal-like states drives metastasis and drug resistance. CDK7 is the serine/threonine kinase of the basal transcription factor TFIIH. We show that dedifferentiation of melanocytic-type melanoma cells into mesenchymal-like cells and acquisition of tolerance to targeted therapies is achieved through chronic inhibition of CDK7. In addition to emergence of a mesenchymal-type signature, we identify a GATA6-dependent gene expression program comprising genes such as AMIGO2 or ABCG2 involved in melanoma survival or targeted drug tolerance, respectively. Mechanistically, we show that CDK7 drives expression of the melanocyte lineage transcription factor MITF that in turn binds to an intronic region of GATA6 to repress its expression in melanocytic-type cells. We show that GATA6 expression is activated in MITF-low melanoma cells of patient-derived xenografts. Taken together, our data show how the poorly characterized repressive function of MITF in melanoma participates in a molecular cascade regulating activation of a transcriptional program involved in survival and drug resistance in melanoma.
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Affiliation(s)
- Pietro Berico
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Max Cigrang
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Guillaume Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Cathy Braun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jeremy Sandoz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Stephanie Legras
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bujamin Hektor Vokshi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nevena Slovic
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - François Peyresaubes
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Carlos Mario Gene Robles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Jean-Marc Egly
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Emmanuel Compe
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Irwin Davidson
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Frederic Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Strasbourg, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, Illkirch, France.,Université de Strasbourg, Illkirch, France
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17
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Yu Y, Tao M, Xu L, Cao L, Le B, An N, Dong J, Xu Y, Yang B, Li W, Liu B, Wu Q, Lu Y, Xie Z, Lian X. Systematic screening reveals synergistic interactions that overcome MAPK inhibitor resistance in cancer cells. Cancer Biol Med 2021; 19:j.issn.2095-3941.2020.0560. [PMID: 34106558 PMCID: PMC8832956 DOI: 10.20892/j.issn.2095-3941.2020.0560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/13/2021] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVE Effective adjuvant therapeutic strategies are urgently needed to overcome MAPK inhibitor (MAPKi) resistance, which is one of the most common forms of resistance that has emerged in many types of cancers. Here, we aimed to systematically identify the genetic interactions underlying MAPKi resistance, and to further investigate the mechanisms that produce the genetic interactions that generate synergistic MAPKi resistance. METHODS We conducted a comprehensive pair-wise sgRNA-based high-throughput screening assay to identify synergistic interactions that sensitized cancer cells to MAPKi, and validated 3 genetic combinations through competitive growth, cell viability, and spheroid formation assays. We next conducted Kaplan-Meier survival analysis based on The Cancer Genome Atlas database and conducted immunohistochemistry to determine the clinical relevance of these synergistic combinations. We also investigated the MAPKi resistance mechanisms of these validated synergistic combinations by using co-immunoprecipitation, Western blot, qRT-PCR, and immunofluorescence assays. RESULTS We constructed a systematic interaction network of MAPKi resistance and identified 3 novel synergistic combinations that effectively targeted MAPKi resistance (ITGB3 + IGF1R, ITGB3 + JNK, and HDGF + LGR5). We next analyzed their clinical relevance and the mechanisms by which they sensitized cancer cells to MAPKi exposure. Specifically, we discovered a novel protein complex, HDGF-LGR5, that adaptively responded to MAPKi to enhance cancer cell stemness, which was up- or downregulated by the inhibitors of ITGB3 + JNK or ITGB3 + IGF1R. CONCLUSIONS Pair-wise sgRNA library screening provided systematic insights into elucidating MAPKi resistance in cancer cells. ITGB3- + IGF1R-targeting drugs (cilengitide + linsitinib) could be used as an effective therapy for suppressing the adaptive formation of the HDGF-LGR5 protein complex, which enhanced cancer stemness during MAPKi stress.
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Affiliation(s)
- Yu Yu
- Department of Cell Biology, Basic Medical College, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Minzhen Tao
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Libin Xu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Lei Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Baoyu Le
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Na An
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Jilin Dong
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Yajie Xu
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Baoxing Yang
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Wei Li
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Bing Liu
- Beijing Syngentech Co., Ltd, Beijing 102206, China
| | - Qiong Wu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yinying Lu
- The Comprehensive Liver Cancer Center, The 5th Medical Center of PLA General Hospital, Beijing 100039, China
| | - Zhen Xie
- MOE Key Laboratory of Bioinformatics and Bioinformatics Division, Center for Synthetic and System Biology, Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing 100084, China
| | - Xiaohua Lian
- Department of Cell Biology, Basic Medical College, Army Medical University (Third Military Medical University), Chongqing 400038, China
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Geny S, Pichard S, Brion A, Renaud JB, Jacquemin S, Concordet JP, Poterszman A. Tagging Proteins with Fluorescent Reporters Using the CRISPR/Cas9 System and Double-Stranded DNA Donors. Methods Mol Biol 2021; 2247:39-57. [PMID: 33301111 DOI: 10.1007/978-1-0716-1126-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Macromolecular complexes govern the majority of biological processes and are of great biomedical relevance as factors that perturb interaction networks underlie a number of diseases, and inhibition of protein-protein interactions is a common strategy in drug discovery. Genome editing technologies enable precise modifications in protein coding genes in mammalian cells, offering the possibility to introduce affinity tags or fluorescent reporters for proteomic or imaging applications in the bona fide cellular context. Here we describe a streamlined procedure which uses the CRISPR/Cas9 system and a double-stranded donor plasmid for efficient generation of homozygous endogenously GFP-tagged human cell lines. Establishing cellular models that preserve native genomic regulation of the target protein is instrumental to investigate protein localization and dynamics using fluorescence imaging but also to affinity purify associated protein complexes using anti-GFP antibodies or nanobodies.
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Affiliation(s)
- Sylvain Geny
- Laboratoire Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), U1154, Centre National de la Recherche Scientifique (CNRS), UMR7196 , Paris, France
| | - Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Alice Brion
- Laboratoire Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), U1154, Centre National de la Recherche Scientifique (CNRS), UMR7196 , Paris, France
| | - Jean-Baptiste Renaud
- Laboratoire Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), U1154, Centre National de la Recherche Scientifique (CNRS), UMR7196 , Paris, France
| | - Sophie Jacquemin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Equipe labellisée Ligue Contre le Cancer, Centre National de la Recherche Scientifique (CNRS), UMR 7104, Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, Université de Strasbourg, Illkirch, France
| | - Jean-Paul Concordet
- Laboratoire Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle (MNHN), Institut National de la Santé et de la Recherche Médicale (INSERM), U1154, Centre National de la Recherche Scientifique (CNRS), UMR7196 , Paris, France.
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Center for Integrated Biology, Integrated Structural Biology Department, Equipe labellisée Ligue Contre le Cancer, CNRS UMR 7104 - Inserm U 1258, University of Strasbourg, Illkirch, France.
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19
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Kour A, Sambyal V, Guleria K, Singh NR, Uppal MS, Manjari M, Sudan M. In silico pathway analysis based on chromosomal instability in breast cancer patients. BMC Med Genomics 2020; 13:168. [PMID: 33167967 PMCID: PMC7653868 DOI: 10.1186/s12920-020-00811-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/11/2020] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Complex genomic changes that arise in tumors are a consequence of chromosomal instability. In tumor cells genomic aberrations disrupt core signaling pathways involving various genes, thus delineating of signaling pathways can help understand the pathogenesis of cancer. The bioinformatics tools can further help in identifying networks of interactions between the genes to get a greater biological context of all genes affected by chromosomal instability. METHODS Karyotypic analyses was done in 150 clinically confirmed breast cancer patients and 150 age and gender matched healthy controls after 72 h Peripheral lymphocyte culturing and GTG-banding. Reactome database from Cytoscape software version 3.7.1 was used to perform in-silico analysis (functional interaction and gene enrichment). RESULTS Frequency of chromosomal aberrations (structural and numerical) was found to be significantly higher in patients as compared to controls. The genes harbored by chromosomal regions showing increased aberration frequency in patients were further analyzed in-silico. Pathway analysis on a set of genes that were not linked together revealed that genes HDAC3, NCOA1, NLRC4, COL1A1, RARA, WWTR1, and BRCA1 were enriched in the RNA Polymerase II Transcription pathway which is involved in recruitment, initiation, elongation and dissociation during transcription. CONCLUSION The current study employs the information inferred from chromosomal instability analysis in a non-target tissue for determining the genes and the pathways associated with breast cancer. These results can be further extrapolated by performing either mutation analysis in the genes/pathways deduced or expression analysis which can pinpoint the relevant functional impact of chromosomal instability.
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Affiliation(s)
- Akeen Kour
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Vasudha Sambyal
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
| | - Kamlesh Guleria
- Human Cytogenetics Laboratory, Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Neeti Rajan Singh
- Department of Surgery, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Manjit Singh Uppal
- Department of Surgery, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Mridu Manjari
- Department of Pathology, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
| | - Meena Sudan
- Department of Radiotherapy, Sri Guru Ram Das Institute of Medical Sciences and Research, Vallah, Amritsar, Punjab, India
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20
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Gupta R, Janostiak R, Wajapeyee N. Transcriptional regulators and alterations that drive melanoma initiation and progression. Oncogene 2020; 39:7093-7105. [PMID: 33024276 PMCID: PMC7695596 DOI: 10.1038/s41388-020-01490-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 09/24/2020] [Indexed: 12/23/2022]
Abstract
Although melanoma is the least frequent type of skin cancer, it accounts for the majority of skin cancer-related deaths. Large-scale sequencing efforts have led to the classification of melanoma into four major subtypes (i.e., BRAF-mutant, NRAS-mutant, NF1-deficient, and triple wild-type). These sequencing studies have also revealed that melanoma genomes are some of the most mutated genomes of all cancers and therefore have a high neoantigen load. These findings have resulted in the development and clinical use of targeted therapies against the oncogenic BRAF→MEK→ERK pathway and immune checkpoint inhibitors for the treatment of metastatic melanoma. Although some patients with metastatic melanoma benefit immensely from these transformative therapies, others either become resistant or do not respond at all. These clinical challenges have intensified the search for new drug targets and drugs that can benefit patients who are either intrinsically resistant or have acquired resistance to targeted therapies and immunotherapies. Numerous signaling pathways and oncogenic drivers can cause changes in mRNA transcription that in turn drive melanoma initiation and progression. Transcriptional regulation of mRNA expression is necessary to maintain cell identity and cellular plasticity via the regulation of transcription factor expression and function, promoter/enhancer activities, chromatin regulators, and three-dimensional genome organization. Transcriptional deregulation can arise due to genetic and/or non-genetic alterations in the genome. Specifically, these deregulated transcriptional programs can become liabilities for melanoma cells due to their acquired dependencies on these programs for survival, which can be harnessed to develop new therapies for melanoma. In this article, we present an overview of the mechanisms that result in the transcriptional deregulation of mRNA expression in melanoma cells and assess how these changes facilitate melanoma initiation and progression. We also describe how these deregulated transcriptional pathways represent new opportunities for the development of unconventional and potentially impactful treatments for metastatic melanoma.
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Affiliation(s)
- Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Radoslav Janostiak
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Narendra Wajapeyee
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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21
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A lncRNA landscape in breast cancer reveals a potential role for AC009283.1 in proliferation and apoptosis in HER2-enriched subtype. Sci Rep 2020; 10:13146. [PMID: 32753692 PMCID: PMC7403317 DOI: 10.1038/s41598-020-69905-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 07/19/2020] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is the most commonly diagnosed neoplasm in women worldwide with a well-recognized heterogeneous pathology, classified into four molecular subtypes: Luminal A, Luminal B, HER2-enriched and Basal-like, each one with different biological and clinical characteristics. Long non-coding RNAs (lncRNAs) represent 33% of the human transcriptome and play critical roles in breast carcinogenesis, but most of their functions are still unknown. Therefore, cancer research could benefit from continued exploration into the biology of lncRNAs in this neoplasm. We characterized lncRNA expression portraits in 74 breast tumors belonging to the four molecular subtypes using transcriptome microarrays. To infer the biological role of the deregulated lncRNAs in the molecular subtypes, we performed co-expression analysis of lncRNA-mRNA and gene ontology analysis. We identified 307 deregulated lncRNAs in tumor compared to normal tissue and 354 deregulated lncRNAs among the different molecular subtypes. Through co-expression analysis between lncRNAs and protein-coding genes, along with gene enrichment analysis, we inferred the potential function of the most deregulated lncRNAs in each molecular subtype, and independently validated our results taking advantage of TCGA data. Overexpression of the AC009283.1 was observed in the HER2-enriched subtype and it is localized in an amplification zone at chromosome 17q12, suggesting it to be a potential tumorigenic lncRNA. The functional role of lncRNA AC009283.1 was examined through loss of function assays in vitro and determining its impact on global gene expression. These studies revealed that AC009283.1 regulates genes involved in proliferation, cell cycle and apoptosis in a HER2 cellular model. We further confirmed these findings through ssGSEA and CEMITool analysis in an independent HER2-amplified breast cancer cohort. Our findings suggest a wide range of biological functions for lncRNAs in each breast cancer molecular subtype and provide a basis for their biological and functional study, as was conducted for AC009283.1, showing it to be a potential regulator of proliferation and apoptosis in the HER2-enriched subtype.
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22
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Lezhava T, Buadze T, Monaselidze J, Jokhadze T, Sigua N, Jangulashvili N, Gaiozishvili M, Koridze M, Zosidze N, Rukhadze M. Epigenetic Changes of Activity of the Ribosomal Cistrons of Human Acrocentric Chromatids in Fetuses, Middle-aged (22–45 years) and Old Individuals (80–106 years). CYTOL GENET+ 2020. [DOI: 10.3103/s009545272003007x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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23
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Uriostegui-Arcos M, Aguayo-Ortiz R, Valencia-Morales MDP, Melchy-Pérez E, Rosenstein Y, Dominguez L, Zurita M. Disruption of TFIIH activities generates a stress gene expression response and reveals possible new targets against cancer. Open Biol 2020; 10:200050. [PMID: 32543350 PMCID: PMC7333893 DOI: 10.1098/rsob.200050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/10/2020] [Indexed: 12/13/2022] Open
Abstract
Disruption of the enzymatic activities of the transcription factor TFIIH by the small molecules Triptolide (TPL) or THZ1 could be used against cancer. Here, we used the MCF10A-ErSrc oncogenesis model to compare the effect of TFIIH inhibitors between transformed cells and their progenitors. We report that tumour cells exhibited highly increased sensitivity to TPL or THZ1 and that the combination of both had a synergic effect. TPL affects the interaction between XPB and p52, causing a reduction in the levels of XPB, p52 and p8, but not other TFIIH subunits. RNA-Seq and RNAPII-ChIP-Seq experiments showed that although the levels of many transcripts were reduced, the levels of a significant number were increased after TPL treatment, with maintained or increased RNAPII promoter occupancy. A significant number of these genes encode for factors that have been related to tumour growth and metastasis, suggesting that transformed cells might rapidly develop resistance to TPL/THZ inhibitors. Some of these genes were also overexpressed in response to THZ1, of which depletion enhances the toxicity of TPL, and are possible new targets against cancer.
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Affiliation(s)
- Maritere Uriostegui-Arcos
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Rodrigo Aguayo-Ortiz
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
- Center for Arrhythmia Research, Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - María del Pilar Valencia-Morales
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Erika Melchy-Pérez
- Departamento de Biomedicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Yvonne Rosenstein
- Departamento de Biomedicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
| | - Laura Dominguez
- Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Mario Zurita
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca Morelos 62250, Mexico
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Laham-Karam N, Pinto GP, Poso A, Kokkonen P. Transcription and Translation Inhibitors in Cancer Treatment. Front Chem 2020; 8:276. [PMID: 32373584 PMCID: PMC7186406 DOI: 10.3389/fchem.2020.00276] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/20/2020] [Indexed: 12/12/2022] Open
Abstract
Transcription and translation are fundamental cellular processes that govern the protein production of cells. These processes are generally up regulated in cancer cells, to maintain the enhanced metabolism and proliferative state of these cells. As such cancerous cells can be susceptible to transcription and translation inhibitors. There are numerous druggable proteins involved in transcription and translation which make lucrative targets for cancer drug development. In addition to proteins, recent years have shown that the "undruggable" transcription factors and RNA molecules can also be targeted to hamper the transcription or translation in cancer. In this review, we summarize the properties and function of the transcription and translation inhibitors that have been tested and developed, focusing on the advances of the last 5 years. To complement this, we also discuss some of the recent advances in targeting oncogenes tightly controlling transcription including transcription factors and KRAS. In addition to natural and synthetic compounds, we review DNA and RNA based approaches to develop cancer drugs. Finally, we conclude with the outlook to the future of the development of transcription and translation inhibitors.
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Affiliation(s)
- Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Gaspar P. Pinto
- International Clinical Research Center, St. Anne University Hospital, Brno, Czechia
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
- University Hospital Tübingen, Department of Internal Medicine VIII, University of Tübingen, Tübingen, Germany
| | - Piia Kokkonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
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25
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Ren J, Liu Y, Wang S, Wang Y, Li W, Chen S, Cui D, Yang S, Li MY, Feng B, Lai PBS, Chen GG. The FKH domain in FOXP3 mRNA frequently contains mutations in hepatocellular carcinoma that influence the subcellular localization and functions of FOXP3. J Biol Chem 2020; 295:5484-5495. [PMID: 32198183 PMCID: PMC7170510 DOI: 10.1074/jbc.ra120.012518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/12/2020] [Indexed: 01/16/2023] Open
Abstract
The transcription factor forkhead box P3 (FOXP3) is a biomarker for regulatory T cells and can also be expressed in cancer cells, but its function in cancer appears to be divergent. The role of hepatocyte-expressed FOXP3 in hepatocellular carcinoma (HCC) is unknown. Here, we collected tumor samples and clinical information from 115 HCC patients and used five human cancer cell lines. We examined FOXP3 mRNA sequences for mutations, used a luciferase assay to assess promoter activities of FOXP3's target genes, and employed mouse tumor models to confirm in vitro results. We detected mutations in the FKH domain of FOXP3 mRNAs in 33% of the HCC tumor tissues, but in none of the adjacent nontumor tissues. None of the mutations occurred at high frequency, indicating that they occurred randomly. Notably, the mutations were not detected in the corresponding regions of FOXP3 genomic DNA, and many of them resulted in amino acid substitutions in the FKH region, altering FOXP3's subcellular localization. FOXP3 delocalization from the nucleus to the cytoplasm caused loss of transcriptional regulation of its target genes, inactivated its tumor-inhibitory capability, and changed cellular responses to histone deacetylase (HDAC) inhibitors. More complex FKH mutations appeared to be associated with worse prognosis in HCC patients. We conclude that mutations in the FKH domain of FOXP3 mRNA frequently occur in HCC and that these mutations are caused by errors in transcription and are not derived from genomic DNA mutations. Our results suggest that transcriptional mutagenesis of FOXP3 plays a role in HCC.
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Affiliation(s)
- Jianwei Ren
- Department of Surgery, Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute (SZRI), Chinese University of Hong Kong, Shenzhen 518057, China
| | - Yi Liu
- Department of Surgery, Chinese University of Hong Kong, Hong Kong, China; Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China
| | - Shanshan Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yu Wang
- Division of Cellular & Molecular Research, National Cancer Centre, Singapore 169610
| | - Wende Li
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China
| | - Siyu Chen
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou 510663, China
| | - Dexuan Cui
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Shengli Yang
- Union Hospital Tumour Center, Wuhan 430022, China
| | - Ming-Yue Li
- Department of Surgery, Chinese University of Hong Kong, Hong Kong, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou 510320, China
| | - Bo Feng
- School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong, China
| | - Paul B S Lai
- Department of Surgery, Chinese University of Hong Kong, Hong Kong, China.
| | - George G Chen
- Department of Surgery, Chinese University of Hong Kong, Hong Kong, China; Shenzhen Research Institute (SZRI), Chinese University of Hong Kong, Shenzhen 518057, China; Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, China; Department of Otorhinolaryngology, Head and Neck Surgery, Chinese University of Hong Kong, Hong Kong, China.
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Zurita M, Murillo-Maldonado JM. Drosophila as a Model Organism to Understand the Effects during Development of TFIIH-Related Human Diseases. Int J Mol Sci 2020; 21:ijms21020630. [PMID: 31963603 PMCID: PMC7013941 DOI: 10.3390/ijms21020630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/02/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022] Open
Abstract
Human mutations in the transcription and nucleotide excision repair (NER) factor TFIIH are linked with three human syndromes: xeroderma pigmentosum (XP), trichothiodystrophy (TTD) and Cockayne syndrome (CS). In particular, different mutations in the XPB, XPD and p8 subunits of TFIIH may cause one or a combination of these syndromes, and some of these mutations are also related to cancer. The participation of TFIIH in NER and transcription makes it difficult to interpret the different manifestations observed in patients, particularly since some of these phenotypes may be related to problems during development. TFIIH is present in all eukaryotic cells, and its functions in transcription and DNA repair are conserved. Therefore, Drosophila has been a useful model organism for the interpretation of different phenotypes during development as well as the understanding of the dynamics of this complex. Interestingly, phenotypes similar to those observed in humans caused by mutations in the TFIIH subunits are present in mutant flies, allowing the study of TFIIH in different developmental processes. Furthermore, studies performed in Drosophila of mutations in different subunits of TFIIH that have not been linked to any human diseases, probably because they are more deleterious, have revealed its roles in differentiation and cell death. In this review, different achievements made through studies in the fly to understand the functions of TFIIH during development and its relationship with human diseases are analysed and discussed.
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27
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Aberrant activation of RPB1 is critical for cell overgrowth in acute myeloid leukemia. Exp Cell Res 2019; 384:111653. [DOI: 10.1016/j.yexcr.2019.111653] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
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28
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Ismael M, Webb R, Ajaz M, Kirkby KJ, Coley HM. The Targeting of RNA Polymerase I Transcription Using CX-5461 in Combination with Radiation Enhances Tumour Cell Killing Effects in Human Solid Cancers. Cancers (Basel) 2019; 11:cancers11101429. [PMID: 31557908 PMCID: PMC6826960 DOI: 10.3390/cancers11101429] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/04/2019] [Accepted: 09/13/2019] [Indexed: 12/04/2022] Open
Abstract
An increased rate of cellular proliferation is a hallmark of cancer and may be accompanied by an increase in ribosome biogenesis and dysregulation in rRNA synthesis. In this regard, CX-5461 has been developed as a novel RNA polymerase I inhibitor and is currently in Phase I/II clinical trials for solid and hematological malignancies. In the present study, interactions between CX-5461 and single-dose X-ray exposure were assessed using isobologram analysis using MTS assay and drug-induced cell death was assessed using flow cytometric, confocal microscopy and Western blot analysis. Combination treatments involving CX-5461 and single-dose X-ray exposure highlighted increased effectiveness compared to individual treatment alone in the CaSki cervical cancer line, with marked synergistic interaction occurring within the low-drug (50 nM) and low-dose radiation range (2–6 Gy). Cell lines challenged with CX-5461 demonstrated the presence of DNA damage, induction of apoptosis, autophagy and senescence alongside high percentages of G2/M cell cycle arrest. In addition, we report preferential sensitivity of ovarian cancer cells with BRCA2 mutation to this novel agent. Taken together, CX-5461 displayed a broad spectrum of activity in a panel of solid cancer cell lines with IC50 values ranging from 35 nM to >1 µM. The work described herein identifies the synergistic effects of CX-5461 in combination with X-rays in solid cancers and may also aid in the design of clinical trials involving this novel agent.
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Affiliation(s)
- Mohammed Ismael
- Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Roger Webb
- Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Mazhar Ajaz
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
| | - Karen J Kirkby
- Ion Beam Centre, Advanced Technology Institute, University of Surrey, Guildford, Surrey GU2 7XH, UK.
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK.
| | - Helen M Coley
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK.
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Donnio LM, Miquel C, Vermeulen W, Giglia-Mari G, Mari PO. Cell-type specific concentration regulation of the basal transcription factor TFIIH in XPB y/y mice model. Cancer Cell Int 2019; 19:237. [PMID: 31516394 PMCID: PMC6734240 DOI: 10.1186/s12935-019-0945-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/18/2019] [Indexed: 11/15/2022] Open
Abstract
Background The basal transcription/repair factor TFIIH is a ten sub-unit complex essential for RNA polymerase II (RNAP2) transcription initiation and DNA repair. In both these processes TFIIH acts as a DNA helix opener, required for promoter escape of RNAP2 in transcription initiation, and to set the stage for strand incision within the nucleotide excision repair (NER) pathway. Methods We used a knock-in mouse model that we generated and that endogenously expresses a fluorescent version of XPB (XPB-YFP). Using different microscopy, cellular biology and biochemistry approaches we quantified the steady state levels of this protein in different cells, and cells imbedded in tissues. Results Here we demonstrate, via confocal imaging of ex vivo tissues and cells derived from this mouse model, that TFIIH steady state levels are tightly regulated at the single cell level, thus keeping nuclear TFIIH concentrations remarkably constant in a cell type dependent manner. Moreover, we show that individual cellular TFIIH levels are proportional to the speed of mRNA production, hence to a cell’s transcriptional activity, which we can correlate to proliferation status. Importantly, cancer tissue presents a higher TFIIH than normal healthy tissues. Conclusion This study shows that TFIIH cellular concentration can be used as a bona-fide quantitative marker of transcriptional activity and cellular proliferation.
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Affiliation(s)
- Lise-Marie Donnio
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
| | - Catherine Miquel
- 2Pathology Department, Saint-Louis Hospital, Université de Paris, 1 Avenue Claude Vellefaux, 75010 Paris, France
| | - Wim Vermeulen
- 3Department of Genetics, Erasmus MC, Dr Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Giuseppina Giglia-Mari
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
| | - Pierre-Olivier Mari
- 1Institut NeuroMyoGène (INMG), CNRS, UMR 5310, INSERM U1217, Faculté de Médecine, Université Claude Bernard Lyon 1, 8 Avenue Rockefeller, 69008 LYON, France
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HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. Sci Rep 2019; 9:9237. [PMID: 31270435 PMCID: PMC6610092 DOI: 10.1038/s41598-019-45349-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/03/2019] [Indexed: 01/02/2023] Open
Abstract
Recent data indicate that up-to 30–40% of cancers can be prevented by dietary and lifestyle measures alone. Herein, we introduce a unique network-based machine learning platform to identify putative food-based cancer-beating molecules. These have been identified through their molecular biological network commonality with clinically approved anti-cancer therapies. A machine-learning algorithm of random walks on graphs (operating within the supercomputing DreamLab platform) was used to simulate drug actions on human interactome networks to obtain genome-wide activity profiles of 1962 approved drugs (199 of which were classified as “anti-cancer” with their primary indications). A supervised approach was employed to predict cancer-beating molecules using these ‘learned’ interactome activity profiles. The validated model performance predicted anti-cancer therapeutics with classification accuracy of 84–90%. A comprehensive database of 7962 bioactive molecules within foods was fed into the model, which predicted 110 cancer-beating molecules (defined by anti-cancer drug likeness threshold of >70%) with expected capacity comparable to clinically approved anti-cancer drugs from a variety of chemical classes including flavonoids, terpenoids, and polyphenols. This in turn was used to construct a ‘food map’ with anti-cancer potential of each ingredient defined by the number of cancer-beating molecules found therein. Our analysis underpins the design of next-generation cancer preventative and therapeutic nutrition strategies.
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Yu Q, Wang P, Yang L, Wu Z, Li S, Xu Y, Wu B, Ma A, Gan X, Xu R. Novel synthetic tosyl chloride-berbamine regresses lethal MYC-positive leukemia by targeting CaMKIIγ/Myc axis. Biomed Pharmacother 2019; 117:109134. [PMID: 31247466 DOI: 10.1016/j.biopha.2019.109134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 01/05/2023] Open
Abstract
Proto-oncogene Myc, a key transcription factor, is frequently deregulated in human leukemia with aggressive and poor clinical outcome, but the development of MYC inhibitors remains challenging due to MYC helix-loop-helix topology lacking druggable domains. Here we describe a novel oral active small molecule analog of berbamine, tosyl chloride-berbamine (TCB), that efficiently eliminates MYC-positive leukemia in vitro and in vivo. Mechanistically, TCB potently reduced MYC protein by inhibiting CaMKIIγ, a critical enzyme that stabilizes MYC protein, and induces apoptosis of MYC-positive leukemia cells. In vivo, oral administration of TCB markedly eliminated lethal MYC-positive acute lymphoblastic leukemia (ALL) with well tolerability in orthotopic mouse model. Our studies identify CaMKIIγ/Myc axis as a valid target for developing small molecule-based new therapies for treating MYC-mediated leukemia and demonstrate that TCB is an orally active analog of berbamine that kills MYC-positive leukemia cells.
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Affiliation(s)
- Qingfeng Yu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Ping Wang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Linlin Yang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Zhaoxing Wu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Shu Li
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Ying Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Bowen Wu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - An Ma
- Zhejiang Academy of Medical Sciences, Hangzhou, 310012, China
| | - Xiaoxian Gan
- Zhejiang Academy of Medical Sciences, Hangzhou, 310012, China
| | - Rongzhen Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China; Institute of Hematology, Zhejiang University, Hangzhou, 310009, China.
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Wang K, Wang X, Hou Y, Zhou H, Mai K, He G. Apoptosis of cancer cells is triggered by selective crosslinking and inhibition of receptor tyrosine kinases. Commun Biol 2019; 2:231. [PMID: 31263775 PMCID: PMC6588694 DOI: 10.1038/s42003-019-0484-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/23/2019] [Indexed: 12/12/2022] Open
Abstract
Receptor tyrosine kinases (RTK) have been the most prevalent therapeutic targets in anti-cancer drug development. However, the emergence of drug resistance toward single target RTK inhibitors remains a major challenge to achieve long-term remissions. Development of alternative RTK inhibitory strategies that bypass drug resistance is much wanted. In the present study, we found that selected cell surface RTKs were inhibited and crosslinked into detergent resistant complexes by oligomeric but not monomeric concanavalin A (ConA). The inhibition of RTKs by ConA led to suppression of pro-survival pathways and induction of apoptosis in multiple cancer cell lines, while overexpression of constitutively activated protein kinase B (AKT) reversed the apoptotic effect. However, major cell stress sensing checkpoints were not influenced by ConA. To our knowledge, selective crosslinking and inhibition of cell surface receptors by ConA-like molecules might represent a previously unidentified mechanism that could be potentially exploited for therapeutic development.
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Affiliation(s)
- Kaidi Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
| | - Xuan Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
| | - Yiying Hou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
| | - Huihui Zhou
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
| | - Kangsen Mai
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
| | - Gen He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, 266003 Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, 266003 Qingdao, China
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Zanconato F, Battilana G, Forcato M, Filippi L, Azzolin L, Manfrin A, Quaranta E, Di Biagio D, Sigismondo G, Guzzardo V, Lejeune P, Haendler B, Krijgsveld J, Fassan M, Bicciato S, Cordenonsi M, Piccolo S. Transcriptional addiction in cancer cells is mediated by YAP/TAZ through BRD4. Nat Med 2018; 24:1599-1610. [PMID: 30224758 PMCID: PMC6181206 DOI: 10.1038/s41591-018-0158-8] [Citation(s) in RCA: 212] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
Abstract
Cancer cells rely on dysregulated gene expression. This establishes specific transcriptional addictions that may be therapeutically exploited. Yet, the mechanisms that are ultimately responsible for these addictions are poorly understood. Here, we investigated the transcriptional dependencies of transformed cells to the transcription factors YAP and TAZ. YAP/TAZ physically engage the general coactivator bromodomain-containing protein 4 (BRD4), dictating the genome-wide association of BRD4 to chromatin. YAP/TAZ flag a large set of enhancers with super-enhancer-like functional properties. YAP/TAZ-bound enhancers mediate the recruitment of BRD4 and RNA polymerase II at YAP/TAZ-regulated promoters, boosting the expression of a host of growth-regulating genes. Treatment with small-molecule inhibitors of BRD4 blunts YAP/TAZ pro-tumorigenic activity in several cell or tissue contexts, causes the regression of pre-established, YAP/TAZ-addicted neoplastic lesions and reverts drug resistance. This work sheds light on essential mediators, mechanisms and genome-wide regulatory elements that are responsible for transcriptional addiction in cancer and lays the groundwork for a rational use of BET inhibitors according to YAP/TAZ biology.
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Affiliation(s)
- Francesca Zanconato
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Giusy Battilana
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Letizia Filippi
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Andrea Manfrin
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Erika Quaranta
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Daniele Di Biagio
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy
| | - Gianluca Sigismondo
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Vincenza Guzzardo
- Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua School of Medicine, Padua, Italy
| | | | | | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ) and Heidelberg University, Heidelberg, Germany
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua School of Medicine, Padua, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Stefano Piccolo
- Department of Molecular Medicine, University of Padua School of Medicine, Padua, Italy.
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy.
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Gervais V, Muller I, Mari PO, Mourcet A, Movellan KT, Ramos P, Marcoux J, Guillet V, Javaid S, Burlet-Schiltz O, Czaplicki G, Milon A, Giglia-Mari G. Small molecule-based targeting of TTD-A dimerization to control TFIIH transcriptional activity represents a potential strategy for anticancer therapy. J Biol Chem 2018; 293:14974-14988. [PMID: 30068551 DOI: 10.1074/jbc.ra118.003444] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/25/2018] [Indexed: 11/06/2022] Open
Abstract
The human transcription factor TFIIH is a large complex composed of 10 subunits that form an intricate network of protein-protein interactions critical for regulating its transcriptional and DNA repair activities. The trichothiodystrophy group A protein (TTD-A or p8) is the smallest TFIIH subunit, shuttling between a free and a TFIIH-bound state. Its dimerization properties allow it to shift from a homodimeric state, in the absence of a functional partner, to a heterodimeric structure, enabling dynamic binding to TFIIH. Recruitment of p8 at TFIIH stabilizes the overall architecture of the complex, whereas p8's absence reduces its cellular steady-state concentration and consequently decreases basal transcription, highlighting that p8 dimerization may be an attractive target for down-regulating transcription in cancer cells. Here, using a combination of molecular dynamics simulations to study p8 conformational stability and a >3000-member library of chemical fragments, we identified small-molecule compounds that bind to the dimerization interface of p8 and provoke its destabilization, as assessed by biophysical studies. Using quantitative imaging of TFIIH in living mouse cells, we found that these molecules reduce the intracellular concentration of TFIIH and its transcriptional activity to levels similar to that observed in individuals with trichothiodystrophy owing to mutated TTD-A Our results provide a proof of concept of fragment-based drug discovery, demonstrating the utility of small molecules for targeting p8 dimerization to modulate the transcriptional machinery, an approach that may help inform further development in anticancer therapies.
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Affiliation(s)
- Virginie Gervais
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France,
| | - Isabelle Muller
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pierre-Olivier Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
| | - Amandine Mourcet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Kumar Tekwani Movellan
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Pascal Ramos
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Julien Marcoux
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Valérie Guillet
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Sumaira Javaid
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France.,the Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center of Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Odile Burlet-Schiltz
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Georges Czaplicki
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Alain Milon
- From the Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, Université Paul Sabatier, BP-64182, F-31077 Toulouse, France
| | - Giuseppina Giglia-Mari
- the Université Claude Bernard Lyon 1, INSERM U1217, Institut NeuroMyoGène, CNRS UMR 5310, F-69008 Lyon, France, and
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Leung AWY, Anantha M, Dragowska WH, Wehbe M, Bally MB. Copper-CX-5461: A novel liposomal formulation for a small molecule rRNA synthesis inhibitor. J Control Release 2018; 286:1-9. [PMID: 30016731 DOI: 10.1016/j.jconrel.2018.07.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 07/04/2018] [Accepted: 07/13/2018] [Indexed: 12/23/2022]
Abstract
CX-5461 is currently in Phase I/II clinical trials for advanced hematologic malignancies and triple negative or BRCA-deficient breast cancer. The compound is currently administered to patients intravenously (i.v.) at low pH (3.5) due to solubility challenges. Reliance of low pH to enhance solubility of CX-5461 can adversely impact pharmacokinetics, biodistribution and therapeutic potential. We have addressed this solubility issue through a formulation method that relies on the interactions between CX-5461 and copper. Copper binds CX-5461 through the nitrogens of the pyrazine ring. Here, we describe synthesizing this copper-complexed CX-5461 (Cu(CX-5461)) within liposomes. CX-5461 was added to copper-containing liposomes and incubated at 60 °C for 30 min. The pharmacokinetics of CX-5461 was assessed in mice following a single i.v. injection at 30 mg/kg. Efficacy studies were completed in multiple subcutaneous mouse xenografts as well as in a bone marrow engraftment model of acute myeloid leukemia (AML). The novel Cu(CX-5461) formulation was stable at pH 7.4 and exhibited increased plasma circulation longevity, increasing the total exposure to CX5461 by an order of magnitude. Cu(CX-5461) was more active than CX-5461 in AML models in vivo. In HCT116-B46 and Capan-1 solid tumour models that are BRCA-deficient, the Cu(CX-5461) formulation engendered activity that was comparable to that of the low pH CX-5461 formulation. We have generated the first Cu(CX-5461) formulation suitable for i.v. administration that is more efficacious than the existing low-pH formulation in pre-clinical models of AML. The Cu(CX-5461) formulation may serve as an alternative formulation for CX-5461 in BRCA-deficient cancers.
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Affiliation(s)
- Ada W Y Leung
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Chemistry, University of British Columbia, Vancouver, BC, Canada; Cuprous Pharmaceuticals Inc., Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Malathi Anantha
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Wieslawa H Dragowska
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Mohamed Wehbe
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Marcel B Bally
- Experimental Therapeutics, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Cuprous Pharmaceuticals Inc., Vancouver, BC, Canada; Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada; Centre for Drug Research and Development, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
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Abstract
Receptor tyrosine kinase signalling pathways have been successfully targeted to inhibit proliferation and angiogenesis for cancer therapy. However, kinase deregulation has been firmly demonstrated to play an essential role in virtually all major disease areas. Kinase inhibitor drug discovery programmes have recently broadened their focus to include an expanded range of kinase targets and therapeutic areas. In this Review, we provide an overview of the novel targets, biological processes and disease areas that kinase-targeting small molecules are being developed against, highlight the associated challenges and assess the strategies and technologies that are enabling efficient generation of highly optimized kinase inhibitors.
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Geist L, Mayer M, Cockcroft XL, Wolkerstorfer B, Kessler D, Engelhardt H, McConnell DB, Konrat R. Direct NMR Probing of Hydration Shells of Protein Ligand Interfaces and Its Application to Drug Design. J Med Chem 2017; 60:8708-8715. [DOI: 10.1021/acs.jmedchem.7b00845] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural
Biology and Biotechnology, Department of Structural and Computational
Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Xiao-Ling Cockcroft
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural
Biology and Biotechnology, Department of Structural and Computational
Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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Di Giovanni C, Novellino E, Chilin A, Lavecchia A, Marzaro G. Investigational drugs targeting cyclin-dependent kinases for the treatment of cancer: an update on recent findings (2013-2016). Expert Opin Investig Drugs 2017; 25:1215-30. [PMID: 27606939 DOI: 10.1080/13543784.2016.1234603] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Cell cycle and gene transcription are under the control of cyclin-dependent kinases (CDKs), whose activity depends on the binding with cyclins. Deregulated CDK activities have been reported in a majority of human cancers, representing potential therapeutic targets. AREAS COVERED This review provides preclinical and clinical (phase I/II) updates of promising therapeutic compounds targeting CDKs published between 2013 and 2016 EXPERT OPINION: First generation pan-CDK inhibitors showed marked toxicity in clinical trials and most compounds were discontinued. Despite their failure was ascribed also to inadequate patient selection rules, novel pan-CDK inhibitors have entered clinical trials with still poorly defined selection strategies. The most interesting results have been obtained with dual CDK4/6 inhibitors and through a more accurate evaluation of predictive biomarkers, suggesting the usefulness of CDK inhibitors for personalized treatment. The increased knowledge on the roles of CDKs in cell cycle and gene transcription suggests to review also the anticancer potential of first generation CDK inhibitors by defining more appropriate rules for patients engagement. Recent findings has highlighted CDK8 as a novel target for cancer treatment. Indeed some biomarkers for CDK8 inhibition sensitivity have already been proposed. CDK8 inhibition is also supposed to prevent cancer metastasis.
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Affiliation(s)
- Carmen Di Giovanni
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Ettore Novellino
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Adriana Chilin
- b Department of Pharmaceutical and Pharmacological Sciences , University of Padova , Padova , Italy
| | - Antonio Lavecchia
- a Department of Pharmacy , University of Naples Federico II , Naples , Italy
| | - Giovanni Marzaro
- b Department of Pharmaceutical and Pharmacological Sciences , University of Padova , Padova , Italy
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Ayoubi HA, Mahjoubi F, Mirzaei R. Investigation of the human H3.3B ( H3F3B) gene expression as a novel marker in patients with colorectal cancer. J Gastrointest Oncol 2017; 8:64-69. [PMID: 28280610 DOI: 10.21037/jgo.2016.12.12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND H3.3 histone is a replacement histone subtype that is express in entire cell cycle phases and overexpress in transcriptionally active regions, promoter regions, and intergenic or intragenic regulatory elements. This histone encoded by two genes termed H3.3A (H3F3A) and H3.3B (H3F3B). Mutations of these two genes lead to some human cancers such as chondroblastoma, osteosarcoma, and epithelial ovarian cancer. The aims of this study were to quantitatively examine the expression of H3.3B gene in colorectal cancer (CRC) and to correlate their expression level with demographics and clinicopathological characteristics. METHODS We investigated H3.3B gene expression in CRC by relative quantitative real-time polymerase chain reaction (real-time PCR) technique for the first time. For this purpose, total RNA extracted, then cDNA synthesized and H3.3B gene expression was evaluated with specific primers by real-time PCR in tumoral tissues and adjacent normal tissues of 36 patients with CRC, then statistical analysis was performed using SPSS software. RESULTS The results of this study indicated that H3.3B gene significantly overexpressed in tumoral tissue than adjacent normal tissue. Furthermore, statistical analysis represented the significant correlation between the H3.3B gene expression and some of the clinicopathological characteristics. CONCLUSIONS Our study showed that H3.3B gene expression changes can be useful as a probable prognosis biomarker in the early stages of CRC before it metastasized.
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Affiliation(s)
- Habib Allah Ayoubi
- Department of Medical Genetic, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Frouzandeh Mahjoubi
- Department of Medical Genetic, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Rezvan Mirzaei
- Department of General Surgery, Hazrat-e-Rasoul Hospital, Tehran University of Medical Sciences and Health Services, Tehran, Iran
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40
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Cheeseman M, Chessum NEA, Rye CS, Pasqua AE, Tucker M, Wilding B, Evans LE, Lepri S, Richards M, Sharp SY, Ali S, Rowlands M, O’Fee L, Miah A, Hayes A, Henley AT, Powers M, te Poele R, De Billy E, Pellegrino L, Raynaud F, Burke R, van Montfort RLM, Eccles SA, Workman P, Jones K. Discovery of a Chemical Probe Bisamide (CCT251236): An Orally Bioavailable Efficacious Pirin Ligand from a Heat Shock Transcription Factor 1 (HSF1) Phenotypic Screen. J Med Chem 2017; 60:180-201. [PMID: 28004573 PMCID: PMC6014687 DOI: 10.1021/acs.jmedchem.6b01055] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/20/2022]
Abstract
Phenotypic screens, which focus on measuring and quantifying discrete cellular changes rather than affinity for individual recombinant proteins, have recently attracted renewed interest as an efficient strategy for drug discovery. In this article, we describe the discovery of a new chemical probe, bisamide (CCT251236), identified using an unbiased phenotypic screen to detect inhibitors of the HSF1 stress pathway. The chemical probe is orally bioavailable and displays efficacy in a human ovarian carcinoma xenograft model. By developing cell-based SAR and using chemical proteomics, we identified pirin as a high affinity molecular target, which was confirmed by SPR and crystallography.
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Affiliation(s)
- Matthew
D. Cheeseman
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Nicola E. A. Chessum
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Carl S. Rye
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - A. Elisa Pasqua
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Michael
J. Tucker
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Birgit Wilding
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Lindsay E. Evans
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Susan Lepri
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Meirion Richards
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Swee Y. Sharp
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Salyha Ali
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
- Division
of Structural Biology at The Institute of
Cancer Research, London SW7 3RP, United Kingdom
| | - Martin Rowlands
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Lisa O’Fee
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Asadh Miah
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Angela Hayes
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Alan T. Henley
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Marissa Powers
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Robert te Poele
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Emmanuel De Billy
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Loredana Pellegrino
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Florence Raynaud
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Rosemary Burke
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Rob L. M. van Montfort
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
- Division
of Structural Biology at The Institute of
Cancer Research, London SW7 3RP, United Kingdom
| | - Suzanne A. Eccles
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Paul Workman
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
| | - Keith Jones
- Cancer
Research UK Cancer Therapeutics Unit at The Institute of Cancer Research, London SW7 3RP, United Kingdom
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41
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Zurita M, Cruz-Becerra G. TFIIH: New Discoveries Regarding its Mechanisms and Impact on Cancer Treatment. J Cancer 2016; 7:2258-2265. [PMID: 27994662 PMCID: PMC5166535 DOI: 10.7150/jca.16966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 09/30/2016] [Indexed: 12/16/2022] Open
Abstract
The deregulation of gene expression is a characteristic of cancer cells, and malignant cells require very high levels of transcription to maintain their cancerous phenotype and survive. Therefore, components of the basal transcription machinery may be considered as targets to preferentially kill cancerous cells. TFIIH is a multisubunit basal transcription factor that also functions in nucleotide excision repair. The recent discoveries of some small molecules that interfere with TFIIH and that preferentially kill cancer cells have increased researchers' interest to elucidate the complex mechanisms by which TFIIH operates. In this review, we summarize the knowledge generated during the 25 years of TFIIH research, highlighting the recent advances in TFIIH structural and mechanistic analyses that suggest the potential of TFIIH as a target for cancer treatment.
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Affiliation(s)
- Mario Zurita
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
| | - Grisel Cruz-Becerra
- Departamento de Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Cuernavaca, Morelos 62250, México
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42
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Ahmed I, Karedath T, Andrews SS, Al IK, Mohamoud YA, Querleu D, Rafii A, Malek JA. Altered expression pattern of circular RNAs in primary and metastatic sites of epithelial ovarian carcinoma. Oncotarget 2016; 7:36366-36381. [PMID: 27119352 PMCID: PMC5095006 DOI: 10.18632/oncotarget.8917] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/02/2016] [Indexed: 12/31/2022] Open
Abstract
Recently, a class of endogenous species of RNA called circular RNA (circRNA) has been shown to regulate gene expression in mammals and their role in cellular function is just beginning to be understood. To investigate the role of circRNAs in ovarian cancer, we performed paired-end RNA sequencing of primary sites, peritoneal and lymph node metastases from three patients with stage IIIC ovarian cancer. We developed an in-house computational pipeline to identify and characterize the circRNA expression from paired-end RNA-Seq libraries. This pipeline revealed thousands of circular isoforms in Epithelial Ovarian Carcinoma (EOC). These circRNAs are enriched for potentially effective miRNA seed matches. A significantly larger number of circRNAs are differentially expressed between tumor sites than mRNAs. Circular and linear expression exhibits an inverse trend for many cancer related pathways and signaling pathways like NFkB, PI3k/AKT and TGF-β typically activated for mRNA in metastases are inhibited for circRNA expression. Further, circRNAs show a more robust expression pattern across patients than mRNA forms indicating their suitability as biomarkers in highly heterogeneous cancer transcriptomes. The consistency of circular RNA expression may offer new candidates for cancer treatment and prognosis.
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Affiliation(s)
- Ikhlak Ahmed
- Department of Genetic medicine, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Thasni Karedath
- Department of Genetic medicine, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Simeon S. Andrews
- Department of Genetic medicine, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Iman K. Al
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Yasmin Ali Mohamoud
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Denis Querleu
- Department of Gynecologic Oncology, Université Montepllier 1, Montpellier, France
| | - Arash Rafii
- Stem Cell and Microenvironment Laboratory, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
| | - Joel A. Malek
- Department of Genetic medicine, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
- Genomics Core, Weill Cornell Medicine-Qatar, Education City, Ar-Rayyan, Qatar
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43
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Kong X, Sun H, Pan P, Tian S, Li D, Li Y, Hou T. Molecular principle of the cyclin-dependent kinase selectivity of 4-(thiazol-5-yl)-2-(phenylamino) pyrimidine-5-carbonitrile derivatives revealed by molecular modeling studies. Phys Chem Chem Phys 2016; 18:2034-46. [DOI: 10.1039/c5cp05622e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to the high sequence identity of the binding pockets of cyclin-dependent kinases (CDKs), designing highly selective inhibitors towards a specific CDK member remains a big challenge.
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Affiliation(s)
- Xiaotian Kong
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Peichen Pan
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Sheng Tian
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM)
- Soochow University
- Suzhou
- P. R. China
- College of Pharmaceutical Sciences
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44
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Srivastava R, Ahn SH. Modifications of RNA polymerase II CTD: Connections to the histone code and cellular function. Biotechnol Adv 2015; 33:856-72. [PMID: 26241863 DOI: 10.1016/j.biotechadv.2015.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/08/2015] [Accepted: 07/28/2015] [Indexed: 12/24/2022]
Abstract
At the onset of transcription, many protein machineries interpret the cellular signals that regulate gene expression. These complex signals are mostly transmitted to the indispensable primary proteins involved in transcription, RNA polymerase II (RNAPII) and histones. RNAPII and histones are so well coordinated in this cellular function that each cellular signal is precisely allocated to specific machinery depending on the stage of transcription. The carboxy-terminal domain (CTD) of RNAPII in eukaryotes undergoes extensive posttranslational modification, called the 'CTD code', that is indispensable for coupling transcription with many cellular processes, including mRNA processing. The posttranslational modification of histones, known as the 'histone code', is also critical for gene transcription through the reversible and dynamic remodeling of chromatin structure. Notably, the histone code is closely linked with the CTD code, and their combinatorial effects enable the delicate regulation of gene transcription. This review elucidates recent findings regarding the CTD modifications of RNAPII and their coordination with the histone code, providing integrative pathways for the fine-tuned regulation of gene expression and cellular function.
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Affiliation(s)
- Rakesh Srivastava
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea
| | - Seong Hoon Ahn
- Division of Molecular and Life Sciences, College of Science and Technology, Hanyang University, Ansan, Republic of Korea.
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45
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Shah SP, Lonial S, Boise LH. When Cancer Fights Back: Multiple Myeloma, Proteasome Inhibition, and the Heat-Shock Response. Mol Cancer Res 2015; 13:1163-73. [PMID: 26013169 DOI: 10.1158/1541-7786.mcr-15-0135] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/13/2015] [Indexed: 01/01/2023]
Abstract
Multiple myeloma is a plasma cell malignancy with an estimated 26,850 new cases and 11,240 deaths in 2015 in the United States. Two main classes of agents are the mainstays of therapy-proteasome inhibitors (PI) and immunomodulatory drugs (IMiD). Other new targets are emerging rapidly, including monoclonal antibodies and histone deacetylase (HDAC) inhibitors. These therapeutic options have greatly improved overall survival, but currently only 15% to 20% of patients experience long-term progression-free survival or are cured. Therefore, improvement in treatment options is needed. One potential means of improving clinical options is to target resistance mechanisms for current agents. For example, eliminating the cytoprotective heat-shock response that protects myeloma cells from proteasome inhibition may enhance PI-based therapies. The transcription factor heat-shock factor 1 (HSF1) is the master regulator of the heat-shock response. HSF1 is vital in the proteotoxic stress response, and its activation is controlled by posttranslational modifications (PTM). This review details the mechanisms of HSF1 regulation and discusses leveraging that regulation to enhance PI activity.
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Affiliation(s)
- Shardule P Shah
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia
| | - Lawrence H Boise
- Department of Hematology and Medical Oncology, Winship, Cancer Institute of Emory University and the Emory University School of Medicine, Atlanta, Georgia. Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia.
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46
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Goundiam O, Gestraud P, Popova T, De la Motte Rouge T, Fourchotte V, Gentien D, Hupé P, Becette V, Houdayer C, Roman-Roman S, Stern MH, Sastre-Garau X. Histo-genomic stratification reveals the frequent amplification/overexpression of CCNE1 and BRD4 genes in non-BRCAness high grade ovarian carcinoma. Int J Cancer 2015; 137:1890-900. [PMID: 25892415 DOI: 10.1002/ijc.29568] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/13/2015] [Accepted: 03/27/2015] [Indexed: 01/08/2023]
Abstract
The treatment of epithelial ovarian cancer (EOC) is narrowly focused despite the heterogeneity of this disease in which outcomes remain poor. To stratify EOC patients for targeted therapy, we developed an approach integrating expression and genomic analyses including the BRCAness status. Gene expression and genomic profiling were used to identify genes recurrently (>5%) amplified and overexpressed in 105 EOC. The LST (Large-scale State Transition) genomic signature of BRCAness was applied to define molecular subgroups of EOC. Amplified/overexpressed genes clustered mainly in 3q, 8q, 19p and 19q. These changes were generally found mutually exclusive. In the 85 patients for which the genomic signature could be determined, genomic BRCAness was found in 52 cases (61.1%) and non-BRCAness in 33 (38.8%). A striking mutual exclusivity was observed between BRCAness and amplification/overexpression data. Whereas 3q and 8q alterations were preferentially observed in BRCAness EOC, most alterations on chromosome 19 were in non-BRCAness cases. CCNE1 (19q12) and BRD4 (19p13.1) amplification/overexpression was found in 19/33 (57.5%) of non-BRCAness cases. Such disequilibrium was also found in the TCGA EOC data set used for validation. Potential target genes are frequently amplified/overexpressed in non-BRCAness EOC. We report that BRD4, already identified as a target in several tumor models, is a new potential target in high grade non-BRCAness ovarian carcinoma.
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Affiliation(s)
- Oumou Goundiam
- Department of Biopathology, Institut Curie, Paris, France.,EA4340-BCOH, Versailles Saint-Quentin-en-Yvelines University, Guyancourt, France.,Department of Translational Research, Institut Curie, Paris, France
| | - Pierre Gestraud
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, Paris, France.,Mines Paris Tech, Paris, France.,Inserm U900, Paris, France
| | | | | | - Virginie Fourchotte
- Department of Surgery, and on behalf of the Gynecologic Study Group, Institut Curie, Paris, France
| | - David Gentien
- Department of Translational Research, Institut Curie, Paris, France
| | - Philippe Hupé
- Bioinformatics and Computational Systems Biology of Cancer, Institut Curie, Paris, France.,Mines Paris Tech, Paris, France.,Inserm U900, Paris, France.,CNRS UMR 144
| | | | - Claude Houdayer
- Department of Biopathology, Institut Curie, Paris, France.,Inserm U830 Institut Curie, Paris, France.,Université Paris Descartes, Sciences Pharmaceutiques et Biologiques, Sorbonne Paris Cité, Paris, France
| | | | - Marc-Henri Stern
- Department of Biopathology, Institut Curie, Paris, France.,Inserm U830 Institut Curie, Paris, France
| | - Xavier Sastre-Garau
- Department of Biopathology, Institut Curie, Paris, France.,EA4340-BCOH, Versailles Saint-Quentin-en-Yvelines University, Guyancourt, France
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