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Cedro-Tanda A, Gómez-Romero L, de Anda-Jauregui G, Garnica-López D, Alfaro-Mora Y, Sánchez-Xochipa S, García-García EF, Mendoza-Vargas A, Frías-Jiménez EJ, Moreno B, Campos-Romero A, Moreno-Camacho JL, Alcantar-Fernández J, Ortíz-Ramírez J, Benitez-González M, Trejo-González R, Aguirre-Chavarría D, Núñez-Martínez ME, Uribe-Figueroa L, Angulo O, Ruiz R, Hidalgo-Miranda A, Herrera LA. Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City. Viruses 2022; 14:545. [PMID: 35336952 PMCID: PMC8950183 DOI: 10.3390/v14030545] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
Omicron is the most mutated SARS-CoV-2 variant-a factor that can affect transmissibility, disease severity, and immune evasiveness. Its genomic surveillance is important in cities with millions of inhabitants and an economic center, such as Mexico City. Results. From 16 November to 31 December 2021, we observed an increase of 88% in Omicron prevalence in Mexico City. We explored the R346K substitution, prevalent in 42% of Omicron variants, known to be associated with immune escape by monoclonal antibodies. In a phylogenetic analysis, we found several independent exchanges between Mexico and the world, and there was an event followed by local transmission that gave rise to most of the Omicron diversity in Mexico City. A haplotype analysis revealed that there was no association between haplotype and vaccination status. Among the 66% of patients who have been vaccinated, no reported comorbidities were associated with Omicron; the presence of odynophagia and the absence of dysgeusia were significant predictor symptoms for Omicron, and the RT-qPCR Ct values were lower for Omicron. Conclusions. Genomic surveillance is key to detecting the emergence and spread of SARS-CoV-2 variants in a timely manner, even weeks before the onset of an infection wave, and can inform public health decisions and detect the spread of any mutation that may affect therapeutic efficacy.
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Affiliation(s)
- Alberto Cedro-Tanda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Laura Gómez-Romero
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Guillermo de Anda-Jauregui
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- Researchers for Mexico (Previously Cátedras CONACYT para Jóvenes Investigadores), Av. de los Insurgentes Sur 1582, Crédito Constructor, Benito Juárez, Mexico City 03940, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Circuito Centro Cultural S/N, Cd. Universitaria, Delegación Coyoacán, Mexico City 04510, Mexico
| | - Dora Garnica-López
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Yair Alfaro-Mora
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Sonia Sánchez-Xochipa
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Eulices F. García-García
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Alfredo Mendoza-Vargas
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Emmanuel J. Frías-Jiménez
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Bernardo Moreno
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, Culiacan 80000, Mexico; (A.C.-R.); (J.A.-F.)
| | | | | | - Jesús Ortíz-Ramírez
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Mariana Benitez-González
- Hospital General Ajusco Medio, Secretaría de Salud de la Ciudad de México (SEDESA), Encinos 41, Miguel Hidalgo 4ta Secc, Tlalpan, Mexico City 14250, Mexico; (J.O.-R.); (M.B.-G.)
| | - Roxana Trejo-González
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Daniel Aguirre-Chavarría
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Marcela E. Núñez-Martínez
- Centro Médico ABC, Av. Carlos Fernández Graef 154, Santa Fe, Contadero, Cuajimalpa de Morelos, Mexico City 05330, Mexico; (R.T.-G.); (D.A.-C.); (M.E.N.-M.)
| | - Laura Uribe-Figueroa
- Laboratorio Arion Genética, Margaritas 440-Bis, Hacienda de Guadalupe Chimalistac, Chimalistac, Álvaro Obregón, Mexico City 01050, Mexico;
| | - Ofelia Angulo
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Rosaura Ruiz
- Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México (SECTEI), Av Chapultepec 49, Colonia Centro, Cuauhtémoc, Mexico City 06010, Mexico; (O.A.); (R.R.)
| | - Alfredo Hidalgo-Miranda
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
| | - Luis A. Herrera
- Instituto Nacional de Medicina Genómica, Periferico Sur 4809, Arenal Tepepan, Mexico City 14610, Mexico; (A.C.-T.); (L.G.-R.); (G.d.A.-J.); (D.G.-L.); (Y.A.-M.); (S.S.-X.); (E.F.G.-G.); (A.M.-V.); (E.J.F.-J.); (B.M.)
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Av. San Fernando 22, Belisario Domínguez Secc 16, Tlalpan, Mexico City 14080, Mexico
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Damián-Zamacona S, Toledo-Ibelles P, Ibarra-Abundis MZ, Uribe-Figueroa L, Hernández-Lemus E, Macedo-Alcibia KP, Delgado–Coello B, Mas-Oliva J, Reyes-Grajeda JP. Early Transcriptomic Response to LDL and oxLDL in Human Vascular Smooth Muscle Cells. PLoS One 2016; 11:e0163924. [PMID: 27727291 PMCID: PMC5058556 DOI: 10.1371/journal.pone.0163924] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023] Open
Abstract
Background Although nowadays it is well known that the human transcriptome can importantly vary according to external or environmental condition, the reflection of this concept when studying oxidative stress and its direct relationship with gene expression profiling during the process of atherogenesis has not been thoroughly achieved. Objective The ability to analyze genome-wide gene expression through transcriptomics has shown that the genome responds dynamically to diverse stimuli. Here, we describe the transcriptome of human vascular smooth muscle cells (hVSMC) stimulated by native and oxidized low-density lipoprotein (nLDL and oxLDL respectively), with the aim of assessing the early molecular changes that induce a response in this cell type resulting in a transcriptomic transformation. This expression has been demonstrated in atherosclerotic plaques in vivo and in vitro, particularly in the light of the oxidative modification hypothesis of atherosclerosis. Approach and Results Total RNA was isolated with TRIzol reagent (Life Technologies) and quality estimated using an Agilent 2100 bioanalyzer. The transcriptome of hVSMC under different experimental conditions (1,5 and 24 hours for nLDL and oxLDL) was obtained using the GeneChip Human Gene 1.0 ST (Affymetrix) designed to measure gene expression of 28,869 well-annotated genes. A fixed fold-change cut-off corresponding to ± 2 was used to identify genes exhibiting the most significant variation and statistical significance (P< 0.05), and 8 genes validated by qPCR using Taqman probes. Conclusions 10 molecular processes were significantly affected in hVSMC: Apoptosis and cell cycle, extracellular matrix remodeling, DNA repair, cholesterol efflux, cGMP biosynthesis, endocytic mechanisms, calcium homeostasis, redox balance, membrane trafficking and finally, the immune response to inflammation. The evidence we present supporting the hypothesis for the involvement of oxidative modification of several processes and metabolic pathways in atherosclerosis is strengthen by the fact that gene expression patterns obtained when hVSMC are incubated for a long period of time in the presence of nLDL, correspond very much the same as when cells are incubated for a short period of time in the presence of chemically modified oxLDL. Our results indicate that under physiological conditions and directly related to specific environmental conditions, LDL particles most probably suffer chemical modifications that initially serve as an alert signal to overcome a harmful stimulus that with time might get transformed to a pathological pattern and therefore consolidate a pathological condition.
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Affiliation(s)
| | - Paola Toledo-Ibelles
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | | | | | | | | | - Blanca Delgado–Coello
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
| | - Jaime Mas-Oliva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México City, México
- * E-mail: (JPRG); (JMO)
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Martínez-Juárez A, Uribe-Figueroa L, Quintana-Palma M, Razo-Aguilera G, Sevilla-Montoya R. Pure trisomy 2p syndrome in two siblings with an unbalanced translocation and minimal terminal 12q monosomy characterized by high-density microarray. Cytogenet Genome Res 2014; 142:249-54. [PMID: 24751616 DOI: 10.1159/000362141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 11/19/2022] Open
Abstract
Pure partial trisomy 2p patients have rarely been reported. Oligonucleotide array analysis has proved to be important for examining 2p rearrangements to delineate the involved segment and to rule out additional imbalances modifying the phenotype. Here, we report 2 siblings with an unbalanced translocation that led to a partial trisomy 2p (p22.3pter) and a terminal deletion of 12q (q24.33qter). This finding was characterized by the molecular karyotyping of both siblings. The 12q loss spanned approximately 300 kb and did not yield clinical features in our patients. The trisomic region in the short arm of chromosome 2 spanned 32.8 Mb and yielded phenotypic features of pure distal 2p trisomy, notably facial anomalies, growth failure, and psychomotor delay. The clinical features of our patients help to delineate the phenotype of the pure trisomy 2p syndrome. Patient 2 also showed a horseshoe kidney which is a previously unrecognized defect associated with this syndrome.
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Peñuelas-Urquides K, González-Escalante L, Villarreal-Treviño L, Silva-Ramírez B, Gutiérrez-Fuentes DJ, Mojica-Espinosa R, Rangel-Escareño C, Uribe-Figueroa L, Molina-Salinas GM, Dávila-Velderrain J, Castorena-Torres F, Bermúdez de León M, Said-Fernández S. Comparison of gene expression profiles between pansensitive and multidrug-resistant strains of Mycobacterium tuberculosis. Curr Microbiol 2013; 67:362-71. [PMID: 23649743 DOI: 10.1007/s00284-013-0376-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 03/28/2013] [Indexed: 11/25/2022]
Abstract
Mycobacterium tuberculosis has developed resistance to anti-tuberculosis first-line drugs. Multidrug-resistant strains complicate the control of tuberculosis and have converted it into a worldwide public health problem. Mutational studies of target genes have tried to envisage the resistance in clinical isolates; however, detection of these mutations in some cases is not sufficient to identify drug resistance, suggesting that other mechanisms are involved. Therefore, the identification of new markers of susceptibility or resistance to first-line drugs could contribute (1) to specifically diagnose the type of M. tuberculosis strain and prescribe an appropriate therapy, and (2) to elucidate the mechanisms of resistance in multidrug-resistant strains. In order to identify specific genes related to resistance in M. tuberculosis, we compared the gene expression profiles between the pansensitive H37Rv strain and a clinical CIBIN:UMF:15:99 multidrug-resistant isolate using microarray analysis. Quantitative real-time PCR confirmed that in the clinical multidrug-resistant isolate, the esxG, esxH, rpsA, esxI, and rpmI genes were upregulated, while the lipF, groES, and narG genes were downregulated. The modified genes could be involved in the mechanisms of resistance to first-line drugs in M. tuberculosis and could contribute to increased efficiency in molecular diagnosis approaches of infections with drug-resistant strains.
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Affiliation(s)
- K Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Calle 2 de abril 501, Col. Independencia, 64720, Monterrey, Nuevo León, Mexico
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5
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Banerji S, Cibulskis K, Rangel-Escareño C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodríguez-Cuevas SA, Romero-Cordoba SL, Schumacher SE, Stransky N, Thompson KM, Uribe-Figueroa L, Baselga J, Beroukhim R, Polyak K, Sgroi DC, Richardson AL, Jimenez-Sánchez G, Lander ES, Gabriel SB, Garraway LA, Golub TR, Meléndez-Zajgla J, Toker A, Getz G, Meyerson M, Hidalgo-Miranda A. Abstract PL07-01: Molecular profiling of breast cancer in Mexico: Identification of novel therapeutic targets through whole genome sequencing analysis. Cancer Epidemiol Biomarkers Prev 2012. [DOI: 10.1158/1055-9965.disp12-pl07-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Today, more than 55% of the world's breast cancer cases are diagnosed in low and middle-income countries and in 2020, more that 70% of the cases will come from the developing nations. In Mexico, breast cancer-specific mortality doubled during the past 20 years, representing the second-leading cause of death in women between 30 and 59 years and the leading cause of cancer related death in the female population. According to statistics, in Mexico a woman dies due to breast cancer every two hours. Even though breast cancer represents a major public health problem in the developing world, knowledge about the genetic and genomic structure of breast tumors in Mexican or Latin American populations is very limited. In the past four years, we have participated in the Slim Initiative of Genomic Medicine (SIGMA) Project, a collaboration between the Carlos Slim Institute of Health, the Broad Institute, and the National Institute of Genomic Medicine in Mexico city. The goal of the SIGMA project is to characterize the genomic basis of common diseases, including several types of cancer. This effort has focused on the application of whole genome and whole exome sequencing of human tumors. In the case of breast cancer, we have analyzed the whole genomes of 22 tumor/normal tissue pairs and the whole exomes of 103 tumor/normal tissues from Mexican and Vietnamese patients. Sequence analysis led to the novel identification of potential loss of function mutations of the CBFB transcription factor, and deletions of its partner RUNX1, an event which has never been previously reported in breast tumors or in any other epithelial tumor. Of clinical relevance, we also identified a somatic translocation involving MAGI3 and AKT3 in a triple negative breast tumor. Ectopic expression of the fusion transcrip leads to constitutive phosphorylation of downstream GSK and loss of contact inhibition. Most importantly, the activity of the fusion protein can be abrogated by an ATP-competitive small molecule inhibitor of AKT, potentially representing a new therapeutic avenue for these patients. In parallel with sequencing, we have also been working on the analysis of somatic DNA copy number aberrations, messenger RNA expression, and microRNA expression patterns in tumors from Mexican patients. Intrinsic breast cancer sub-typing in 125 tumors from Mexican patients showed that 13.6% of the tumors were basal-like, 16.8% were Her2-enriched, 24.8% Luminal A, 34.4% Luminal B and 10.4 normal-like. With microRNA expression, we have identified a group of microRNAs whose role in breast cancer has not been previously described and are currently analyzing differential microRNA expression across tumor sub-types, in particular triple negative tumors, where we have been able to identify at least three different tumor sub-groups based on microRNA expression patterns.
Citation Format: Shantanu Banerji, Kristian Cibulskis, Claudia Rangel-Escareño, Kristin K. Brown, Scott L. Carter, Abbie M. Frederick, Michael S. Lawrence, Andrey Y. Sivachenko, Carrie Sougnez, Lihua Zou, Maria L. Cortes, Juan C. Fernandez-Lopez, Shouyong Peng, Kristin G. Ardlie, Daniel Auclair, Veronica Bautista-Piña, Fujiko Duke, Joshua Francis, Joonil Jung, Antonio Maffuz-Aziz, Robert C. Onofrio, Melissa Parkin, Nam H. Pho, Valeria Quintanar-Jurado, Alex H. Ramos, Rosa Rebollar-Vega, Sergio A. Rodríguez-Cuevas, Sandra L. Romero-Cordoba, Steven E. Schumacher, Nicolas Stransky, Kristin M. Thompson, Laura Uribe-Figueroa, Jose Baselga, Rameen Beroukhim, Kornelia Polyak, Dennis C. Sgroi, Andrea L. Richardson, Gerardo Jimenez-Sánchez, Eric S. Lander, Stacey B. Gabriel, Levi A. Garraway, Todd R. Golub, Jorge Meléndez-Zajgla, Alex Toker, Gad Getz, Matthew Meyerson, Alfredo Hidalgo-Miranda. Molecular profiling of breast cancer in Mexico: Identification of novel therapeutic targets through whole genome sequencing analysis. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr PL07-01.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Lihua Zou
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | - Fujiko Duke
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Joonil Jung
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | - Nam H. Pho
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Alex H. Ramos
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Todd R. Golub
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
| | | | - Alex Toker
- 3Beth Israel Deaconess Medical Center, Boston, MA,
| | - Gad Getz
- 1The Broad Institute of MIT and Harvard, Cambridge, MA,
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Ibarra Sierra E, Díaz Chávez J, Cortés-Malagón EM, Uribe-Figueroa L, Hidalgo-Miranda A, Lambert PF, Gariglio P. Differential gene expression between skin and cervix induced by the E7 oncoprotein in a transgenic mouse model. Virology 2012; 433:337-45. [PMID: 22980503 DOI: 10.1016/j.virol.2012.08.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/20/2012] [Accepted: 08/17/2012] [Indexed: 10/27/2022]
Abstract
HPV16 E7 oncoprotein expression in K14E7 transgenic mice induces cervical cancer after 6 months of treatment with the co-carcinogen 17β-estradiol. In untreated mice, E7 also induces skin tumors late in life albeit at low penetrance. These findings indicate that E7 alters cellular functions in cervix and skin so as to predispose these organs to tumorigenesis. Using microarrays, we determined the global genes expression profile in cervical and skin tissue of young adult K14E7 transgenic mice without estrogen treatment. In these tissues, the E7 oncoprotein altered the transcriptional pattern of genes involved in several biological processes including signal transduction, transport, metabolic process, cell adhesion, apoptosis, cell differentiation, immune response and inflammatory response. Among the E7-dysregulated genes were ones not previously known to be involved in cervical neoplasia including DMBT1, GLI1 and 17βHSD2 in cervix, as well as MMP2, 12, 14, 19 and 27 in skin.
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Affiliation(s)
- E Ibarra Sierra
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados, México DF, Mexico
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7
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Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, Lawrence MS, Sivachenko AY, Sougnez C, Zou L, Cortes ML, Fernandez-Lopez JC, Peng S, Ardlie KG, Auclair D, Bautista-Piña V, Duke F, Francis J, Jung J, Maffuz-Aziz A, Onofrio RC, Parkin M, Pho NH, Quintanar-Jurado V, Ramos AH, Rebollar-Vega R, Rodriguez-Cuevas S, Romero-Cordoba SL, Schumacher SE, Stransky N, Thompson KM, Uribe-Figueroa L, Baselga J, Beroukhim R, Polyak K, Sgroi DC, Richardson AL, Jimenez-Sanchez G, Lander ES, Gabriel SB, Garraway LA, Golub TR, Melendez-Zajgla J, Toker A, Getz G, Hidalgo-Miranda A, Meyerson M. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 2012; 486:405-9. [PMID: 22722202 PMCID: PMC4148686 DOI: 10.1038/nature11154] [Citation(s) in RCA: 920] [Impact Index Per Article: 76.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 04/20/2012] [Indexed: 12/18/2022]
Abstract
Breast carcinoma is the leading cause of cancer-related mortality in women worldwide, with an estimated 1.38 million new cases and 458,000 deaths in 2008 alone. This malignancy represents a heterogeneous group of tumours with characteristic molecular features, prognosis and responses to available therapy. Recurrent somatic alterations in breast cancer have been described, including mutations and copy number alterations, notably ERBB2 amplifications, the first successful therapy target defined by a genomic aberration. Previous DNA sequencing studies of breast cancer genomes have revealed additional candidate mutations and gene rearrangements. Here we report the whole-exome sequences of DNA from 103 human breast cancers of diverse subtypes from patients in Mexico and Vietnam compared to matched-normal DNA, together with whole-genome sequences of 22 breast cancer/normal pairs. Beyond confirming recurrent somatic mutations in PIK3CA, TP53, AKT1, GATA3 and MAP3K1, we discovered recurrent mutations in the CBFB transcription factor gene and deletions of its partner RUNX1. Furthermore, we have identified a recurrent MAGI3-AKT3 fusion enriched in triple-negative breast cancer lacking oestrogen and progesterone receptors and ERBB2 expression. The MAGI3-AKT3 fusion leads to constitutive activation of AKT kinase, which is abolished by treatment with an ATP-competitive AKT small-molecule inhibitor.
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Affiliation(s)
- Shantanu Banerji
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | | | | | - Kristin K. Brown
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215
| | - Scott L. Carter
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | | | - Carrie Sougnez
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Lihua Zou
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Maria L. Cortes
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Shouyong Peng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | | - Daniel Auclair
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Fujiko Duke
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Joshua Francis
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Joonil Jung
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | - Melissa Parkin
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Nam H. Pho
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Alex H. Ramos
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | | | - Steven E. Schumacher
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Nicolas Stransky
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | | | - Jose Baselga
- Harvard Medical School, Boston, MA, 02115, USA
- Division of Hematology and Oncology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Rameen Beroukhim
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Dennis C. Sgroi
- Harvard Medical School, Boston, MA, 02115, USA
- Depertment of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Andrea L. Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | | | - Eric S. Lander
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | - Levi A. Garraway
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Todd R. Golub
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Alex Toker
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215
| | - Gad Getz
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | | | - Matthew Meyerson
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Harvard Medical School, Boston, MA, 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
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Frigolet ME, Torres N, Uribe-Figueroa L, Rangel C, Jimenez-Sanchez G, Tovar AR. White adipose tissue genome wide-expression profiling and adipocyte metabolic functions after soy protein consumption in rats. J Nutr Biochem 2010; 22:118-29. [PMID: 20471815 DOI: 10.1016/j.jnutbio.2009.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2009] [Revised: 11/27/2009] [Accepted: 12/10/2009] [Indexed: 12/14/2022]
Abstract
Obesity is associated with an increase in adipose tissue mass due to an imbalance between high dietary energy intake and low physical activity; however, the type of dietary protein may contribute to its development. The aim of the present work was to study the effect of soy protein versus casein on white adipose tissue genome profiling, and the metabolic functions of adipocytes in rats with diet-induced obesity. The results showed that rats fed a Soy Protein High-Fat (Soy HF) diet gained less weight and had lower serum leptin concentration than rats fed a Casein High-Fat (Cas HF) diet, despite similar energy intake. Histological studies indicated that rats fed the Soy HF diet had significantly smaller adipocytes than those fed the Cas HF diet, and this was associated with a lower triglyceride/DNA content. Fatty acid synthesis in isolated adipocytes was reduced by the amount of fat consumed but not by the type of protein ingested. Expression of genes of fatty acid oxidation increased in adipose tissue of rats fed Soy diets; microarray analysis revealed that Soy protein consumption modified the expression of 90 genes involved in metabolic functions and inflammatory response in adipose tissue. Network analysis showed that the expression of leptin was regulated by the type of dietary protein and it was identified as a central regulator of the expression of lipid metabolism genes in adipose tissue. Thus, soy maintains the size and metabolic functions of adipose tissue through biochemical adaptations, adipokine secretion, and global changes in gene expression.
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Affiliation(s)
- Maria E Frigolet
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, DF 14000, México
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9
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Mendoza-Villanueva D, Diaz-Chavez J, Uribe-Figueroa L, Rangel-Escareão C, Hidalgo-Miranda A, March-Mifsut S, Jimenez-Sanchez G, Lambert P, Gariglio P. Gene expression profile of cervical and skin tissues from human papillomavirus type 16 E6 transgenic mice. BMC Cancer 2008; 8:347. [PMID: 19036130 PMCID: PMC2610035 DOI: 10.1186/1471-2407-8-347] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 11/26/2008] [Indexed: 02/08/2023] Open
Abstract
Background Although K14E6 transgenic mice develop spontaneous tumors of the skin epithelium, no spontaneous reproductive tract malignancies arise, unless the transgenic mice were treated chronically with 17β-estradiol. These findings suggest that E6 performs critical functions in normal adult cervix and skin, highlighting the need to define E6-controlled transcriptional programs in these tissues. Methods We evaluated the expression profile of 14,000 genes in skin or cervix from young K14E6 transgenic mice compared with nontransgenic. To identify differentially expressed genes a linear model was implemented using R and the LIMMA package. Two criteria were used to select the set of relevant genes. First a set of genes with a Log-odds ≥ 3 were selected. Then, a hierarchical search of genes was based on Log Fold Changes. Results Microarray analysis identified a total of 676 and 1154 genes that were significantly up and down-regulated, respectively, in skin from K14E6 transgenic mice. On the other hand, in the cervix from K14E6 transgenic mice we found that only 97 and 252 genes were significantly up and down-regulated, respectively. One of the most affected processes in the skin from K14E6 transgenic mice was the cell cycle. We also found that skin from transgenic mice showed down-regulation of pro-apoptotic genes and genes related to the immune response. In the cervix of K14E6 transgenic mice, we could not find affected any gene related to the cell cycle and apoptosis pathways but did observe alterations in the expression of immune response genes. Pathways such as angiogenesis, cell junction and epidermis development, also were altered in their gene expression profiles in both tissues. Conclusion Expression of the HPV16 E6 oncoprotein in our model alters expression of genes that fell into several functional groups providing insights into pathways by which E6 deregulate cell cycle progression, apoptosis, the host resistance to infection and immune function, providing new opportunities for early diagnostic markers and therapeutic drug targets.
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Affiliation(s)
- D Mendoza-Villanueva
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados, México DF 07000, México.
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