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Bravo‐Estupiñan DM, Aguilar‐Guerrero K, Quirós S, Acón M, Marín‐Müller C, Ibáñez‐Hernández M, Mora‐Rodríguez RA. Gene dosage compensation: Origins, criteria to identify compensated genes, and mechanisms including sensor loops as an emerging systems-level property in cancer. Cancer Med 2023; 12:22130-22155. [PMID: 37987212 PMCID: PMC10757140 DOI: 10.1002/cam4.6719] [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: 04/24/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The gene dosage compensation hypothesis presents a mechanism through which the expression of certain genes is modulated to compensate for differences in the dose of genes when additional chromosomes are present. It is one of the means through which cancer cells actively cope with the potential damaging effects of aneuploidy, a hallmark of most cancers. Dosage compensation arises through several processes, including downregulation or overexpression of specific genes and the relocation of dosage-sensitive genes. In cancer, a majority of compensated genes are generally thought to be regulated at the translational or post-translational level, and include the basic components of a compensation loop, including sensors of gene dosage and modulators of gene expression. Post-translational regulation is mostly undertaken by a general degradation or aggregation of remaining protein subunits of macromolecular complexes. An increasingly important role has also been observed for transcriptional level regulation. This article reviews the process of targeted gene dosage compensation in cancer and other biological conditions, along with the mechanisms by which cells regulate specific genes to restore cellular homeostasis. These mechanisms represent potential targets for the inhibition of dosage compensation of specific genes in aneuploid cancers. This article critically examines the process of targeted gene dosage compensation in cancer and other biological contexts, alongside the criteria for identifying genes subject to dosage compensation and the intricate mechanisms by which cells orchestrate the regulation of specific genes to reinstate cellular homeostasis. Ultimately, our aim is to gain a comprehensive understanding of the intricate nature of a systems-level property. This property hinges upon the kinetic parameters of regulatory motifs, which we have termed "gene dosage sensor loops." These loops have the potential to operate at both the transcriptional and translational levels, thus emerging as promising candidates for the inhibition of dosage compensation in specific genes. Additionally, they represent novel and highly specific therapeutic targets in the context of aneuploid cancer.
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Affiliation(s)
- Diana M. Bravo‐Estupiñan
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Programa de Doctorado en Ciencias, Sistema de Estudios de Posgrado (SEP)Universidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Karol Aguilar‐Guerrero
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Maestría académica en Microbiología, Programa de Posgrado en Microbiología, Parasitología, Química Clínica e InmunologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Steve Quirós
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
| | - Man‐Sai Acón
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
| | - Christian Marín‐Müller
- Speratum Biopharma, Inc.Centro Nacional de Innovación Biotecnológica Nacional (CENIBiot)San JoséCosta Rica
| | - Miguel Ibáñez‐Hernández
- Laboratorio de Terapia Génica, Departamento de BioquímicaEscuela Nacional de Ciencias Biológicas del Instituto Politécnico NacionalCiudad de MéxicoMexico
| | - Rodrigo A. Mora‐Rodríguez
- CICICA, Centro de Investigación en Cirugía y Cáncer Research Center on Surgery and CancerUniversidad de Costa RicaSan JoséCosta Rica
- Laboratorio de Quimiosensibilidad tumoral (LQT), Centro de Investigación en enfermedades Tropicales (CIET), Facultad de MicrobiologíaUniversidad de Costa RicaSan JoséCosta Rica
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2
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Mohanty V, Wang F, Mills GB, Chen K. Uncoupling of gene expression from copy number presents therapeutic opportunities in aneuploid cancers. Cell Rep Med 2021; 2:100349. [PMID: 34337565 PMCID: PMC8324495 DOI: 10.1016/j.xcrm.2021.100349] [Citation(s) in RCA: 3] [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: 09/28/2020] [Revised: 02/11/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022]
Abstract
Uncoupling of mRNA expression from copy number (UECN) might be a strategy for cancer cells to a tolerate high degree of aneuploidy. To test the extent and role of UECN across cancers, we perform integrative multiomic analysis of The Cancer Genome Atlas (TCGA) dataset, encompassing ∼5,000 individual tumors. We find UECN is common in cancers and is associated with increased oncogenic signaling, proliferation, and immune suppression. UECN appears to be orchestrated by complex regulatory changes, with transcription factors (TFs) playing a prominent role. To further dissect the regulatory mechanisms, we develop a systems-biology approach to identify candidate TFs, which could serve as targets to disrupt UECN and reduce tumor fitness. Applying our approach to TCGA data, we identify 21 putative targets, 42.8% of which are validated by independent sources. Together, our study indicates that UECN is likely an important mechanism in development of aneuploid tumors and might be therapeutically targetable.
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Affiliation(s)
- Vakul Mohanty
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fang Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gordon B. Mills
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - CTD2 Research Network
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health University, Portland, OR 97201, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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3
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Oatman N, Dasgupta N, Arora P, Choi K, Gawali MV, Gupta N, Parameswaran S, Salomone J, Reisz JA, Lawler S, Furnari F, Brennan C, Wu J, Sallans L, Gudelsky G, Desai P, Gebelein B, Weirauch MT, D'Alessandro A, Komurov K, Dasgupta B. Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer. SCIENCE ADVANCES 2021; 7:eabd7459. [PMID: 33568479 PMCID: PMC7875532 DOI: 10.1126/sciadv.abd7459] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/22/2020] [Indexed: 05/22/2023]
Abstract
The lipogenic enzyme stearoyl CoA desaturase (SCD) plays a key role in tumor lipid metabolism and membrane architecture. SCD is often up-regulated and a therapeutic target in cancer. Here, we report the unexpected finding that median expression of SCD is low in glioblastoma relative to normal brain due to hypermethylation and unintentional monoallelic co-deletion with phosphatase and tensin homolog (PTEN) in a subset of patients. Cell lines from this subset expressed undetectable SCD, yet retained residual SCD enzymatic activity. Unexpectedly, these lines evolved to survive independent of SCD through unknown mechanisms. Cell lines that escaped such genetic and epigenetic alterations expressed higher levels of SCD and were highly dependent on SCD for survival. Last, we identify that SCD-dependent lines acquire resistance through a previously unknown FBJ murine osteosarcoma viral oncogene homolog B (FOSB)-mediated mechanism. Accordingly, FOSB inhibition blunted acquired resistance and extended survival of tumor-bearing mice treated with SCD inhibitor.
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Affiliation(s)
- Nicole Oatman
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nupur Dasgupta
- Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Priyanka Arora
- College of Pharmacy, University of Cincinnati, Cincinnati, OH, USA
| | - Kwangmin Choi
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mruniya V Gawali
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nishtha Gupta
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Joseph Salomone
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sean Lawler
- Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Furnari
- Ludwig Institute of Cancer Research, University of California, San Diego, CA, USA
| | | | - Jianqiang Wu
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Larry Sallans
- Department of Chemistry, University of Cincinnati, Cincinnati, OH, USA
| | - Gary Gudelsky
- College of Pharmacy, University of Cincinnati, Cincinnati, OH, USA
| | - Pankaj Desai
- College of Pharmacy, University of Cincinnati, Cincinnati, OH, USA
| | - Brian Gebelein
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kakajan Komurov
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Biplab Dasgupta
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- University of Cincinnati College of Medicine, Cincinnati, OH, USA
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4
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Ben-David U, Amon A. Context is everything: aneuploidy in cancer. Nat Rev Genet 2019; 21:44-62. [DOI: 10.1038/s41576-019-0171-x] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
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Chromosomal Density of Cancer Up-Regulated Genes, Aberrant Enhancer Activity and Cancer Fitness Genes Are Associated with Transcriptional Cis-Effects of Broad Copy Number Gains in Colorectal Cancer. Int J Mol Sci 2019; 20:ijms20184652. [PMID: 31546890 PMCID: PMC6770609 DOI: 10.3390/ijms20184652] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/15/2019] [Accepted: 09/16/2019] [Indexed: 12/31/2022] Open
Abstract
Broad Copy Number Gains (BCNGs) are copy-number increases of chromosomes or large segments of chromosomal arms. Publicly-available single-nucleotide polymorphism (SNP) array and RNA-Seq data of colon adenocarcinoma (COAD) samples from The Cancer Genome Atlas (TCGA) consortium allowed us to design better control groups in order to identify changes in expression due to highly recurrent BCNGs (in chromosomes 20, 8, 7, 13). We identified: (1) Overexpressed Transcripts (OverT), transcripts whose expression increases in "COAD groups bearing a specific BCNG" in comparison to "control COAD groups" not bearing it, and (2) up-regulated/down-regulated transcripts, transcripts whose expression increases/decreases in COAD groups in comparison to normal colon tissue. An analysis of gene expression reveals a correlation between the density of up-regulated genes per selected chromosome and the recurrence rate of their BCNGs. We report an enrichment of gained enhancer activity and of cancer fitness genes among OverT genes. These results support the hypothesis that the chromosomal density of overexpressed cancer fitness genes might play a significant role in the selection of gained chromosomes during cancer evolution. Analysis of functional pathways associated with OverT suggest that some multi-subunit protein complexes (eIF2, eIF3, CSTF and CPSF) are candidate targets for silencing transcriptional therapy.
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Integrated transcriptomic-genomic tool Texomer profiles cancer tissues. Nat Methods 2019; 16:401-404. [PMID: 30988467 DOI: 10.1038/s41592-019-0388-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 03/04/2019] [Indexed: 01/08/2023]
Abstract
Profiling of both the genome and the transcriptome promises a comprehensive, functional readout of a tissue sample, yet analytical approaches are required to translate the increased data dimensionality, heterogeneity and complexity into patient benefits. We developed a statistical approach called Texomer ( https://github.com/KChen-lab/Texomer ) that performs allele-specific, tumor-deconvoluted transcriptome-exome integration of autologous bulk whole-exome and transcriptome sequencing data. Texomer results in substantially improved accuracy in sample categorization and functional variant prioritization.
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Condorelli DF, Spampinato G, Valenti G, Musso N, Castorina S, Barresi V. Positive Caricature Transcriptomic Effects Associated with Broad Genomic Aberrations in Colorectal Cancer. Sci Rep 2018; 8:14826. [PMID: 30287863 PMCID: PMC6172234 DOI: 10.1038/s41598-018-32884-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 09/07/2018] [Indexed: 12/12/2022] Open
Abstract
We re-examined the correlation between Broad Genomic Aberrations (BGAs) and transcriptomic profiles in Colorectal Cancer (CRC). Two types of BGAs have been examined: Broad Copy-Number Abnormal regions (BCNAs), distinguished in gain- and loss-type, and Copy-Neutral Loss of Heterozygosities (CNLOHs). Transcripts are classified as “OverT” or “UnderT” if overexpressed or underexpressed comparing CRCs bearing a specific BGA to CRCs not bearing it and as “UpT” or “DownT” if upregulated or downregulated in cancer compared to normal tissue. BGA-associated effects were evaluated by changes in the “Chromosomal Distribution Index” (CDI) of different transcript classes. Data show that UpT are more sensitive than DownT to BCNA-associated gene dosage effects. “Over-UpT” genes are upregulated in cancer and further overexpressed by gene dosage, defining the so called “positive caricature transcriptomic effect”. When Over-UpT genes are ranked according to overexpression, top positions are occupied by genes implicated at the functional and therapeutic level in CRC. We show that cancer-upregulated transcripts are sensitive markers of BCNA-induced effects and suggest that analysis of positive caricature transcriptomic effects can provide clues toward the identification of BCNA-associated cancer driver genes.
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Affiliation(s)
- Daniele F Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy.
| | - Giorgia Spampinato
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Giovanna Valenti
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy
| | - Sergio Castorina
- Department of Medical and Surgical Sciences and Advanced Technologies, University of Catania, Catania, (95123), Italy
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, (95123), Italy.
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Clissold RL, Ashfield B, Burrage J, Hannon E, Bingham C, Mill J, Hattersley A, Dempster EL. Genome-wide methylomic analysis in individuals with HNF1B intragenic mutation and 17q12 microdeletion. Clin Epigenetics 2018; 10:97. [PMID: 30021660 PMCID: PMC6052548 DOI: 10.1186/s13148-018-0530-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022] Open
Abstract
Heterozygous mutation of the transcription factor HNF1B is the most common cause of monogenetic developmental renal disease. Disease-associated mutations fall into two categories: HNF1B intragenic mutations and a 1.3 Mb deletion at chromosome 17q12. An increase in neurodevelopmental disorders has been observed in individuals harbouring the 17q12 deletion but not in patients with HNF1B coding mutations.Previous investigations have concentrated on identifying a genetic cause for the increase in behavioural problems seen in 17q12 deletion carriers. We have taken the alternative approach of investigating the DNA methylation profile of these two HNF1B genotype groups along with controls matched for age, gender and diabetes status using the Illumina 450K DNA methylation array (total sample n = 60).We identified a number of differentially methylated probes (DMPs) that were associated with HNF1B-associated disease and passed our stringent experiment-wide significance threshold. These associations were largely driven by the deletion patients and the majority of the significant probes mapped to the 17q12 deletion locus. The observed changes in DNA methylation at this locus were not randomly dispersed and occurred in clusters, suggesting a regulatory mechanism reacting to haploinsufficiency across the entire deleted region.Along with these deletion-specific changes in DNA methylation, we also identified a shared DNA methylation signature in both mutation and deletion patient groups indicating that haploinsufficiency of HNF1B impacts on the methylome of a number of genes, giving further insight to the role of HNF1B.
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Affiliation(s)
- Rhian L Clissold
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Beth Ashfield
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Coralie Bingham
- University of Exeter Medical School, University of Exeter, Exeter, UK.,Exeter Kidney Unit, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Andrew Hattersley
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK.
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Marques-Magalhães Â, Graça I, Henrique R, Jerónimo C. Targeting DNA Methyltranferases in Urological Tumors. Front Pharmacol 2018; 9:366. [PMID: 29706891 PMCID: PMC5909196 DOI: 10.3389/fphar.2018.00366] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 03/28/2018] [Indexed: 12/14/2022] Open
Abstract
Urological cancers are a heterogeneous group of malignancies accounting for a considerable proportion of cancer-related morbidity and mortality worldwide. Aberrant epigenetic traits, especially altered DNA methylation patterns constitute a hallmark of these tumors. Nonetheless, these alterations are reversible, and several efforts have been carried out to design and test several epigenetic compounds that might reprogram tumor cell phenotype back to a normal state. Indeed, several DNMT inhibitors are currently under evaluation for therapeutic efficacy in clinical trials. This review highlights the critical role of DNA methylation in urological cancers and summarizes the available data on pre-clinical assays and clinical trials with DNMT inhibitors in bladder, kidney, prostate, and testicular germ cell cancers.
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Affiliation(s)
- Ângela Marques-Magalhães
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Inês Graça
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group - Research Center, Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
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