Unidad de Proteómica

Javier Muñoz Jefe de Unidad
T +34 (+34) 917 328 000 (Ext 3110)
jmunozpe@cnio.es

Becarios Pre-Doctorales

Cristina Sayago

Técnicos de Laboratorio

Elvira Fernández-Vigo
Fernando García
Nuria Ibarz
Jana Sánchez
Álvaro Soriano
Maria Pilar Ximénez de Embún
Eduardo Zarzuela

Proteins are the molecular effectors of cells and catalyse almost all biological processes. The levels of protein abundance, together with their modification states and interactions, adapt dynamically to external or internal ( genetic ) stimuli and thus define the cell’s functional state and determine its phenotype. Mass spectrometry-based proteomics is the most powerful tool to study the proteome, providing fundamental basic biology information. In addition, recent improvements in sensitivity and throughput now enable the analysis of larger cohorts of samples including biopsies, thereby making proteomics a part of the clinical research toolbox. All these efforts are providing new insights into the molecular mechanisms underlying cancer development as well as the identification of novel biomarkers.

Publicaciones

Karras P, Riveiro-Falkenbach E, Cañón E, Tejedo C, Calvo TG, Martínez-Herranz R, Alonso-Curbelo D, Cifdaloz M, Perez-Guijarro E, Gómez-López G, Ximenez-Embun P, Muñoz J, Megias D, Olmeda D, Moscat J, Ortiz-Romero PL, Rodríguez-Peralto JL, Soengas MS. (2019). p62/SQSTM1 Fuels Melanoma Progression by Opposing mRNA Decay of a Selective Set of Pro-metastatic Factors.. Cancer Cell 35, 46-63.
Sayago C, Martinez-Val A, Munoz J (2019). Proteotyping pluripotency with mass spectrometry. Expert Rev Proteomic (in press).
Borghesan M, Fafián-Labora J, Eleftheriadou O, Carpintero-Fernández P, Paez-Ribes M, Vizcay-Barrena G, Swisa A, Kolodkin-Gal D, Ximénez-Embún P, Lowe R, Martín-Martín B, Peinado H, Muñoz J, Fleck RA, Dor Y, Ben-Porath I, Vossenkamper A, Muñoz-Espin D, O'Loghlen A (2019). Small Extracellular Vesicles Are Key Regulators of Non-cell Autonomous Intercellular Communication in Senescence via the Interferon Protein IFITM3.. Cell Reports 27, 3956-3971.
Segura V, Valero ML, Cantero L, Muñoz J, Zarzuela E, García F, Aloria K, Beaskoetxea J, Arizmendi JM, Navajas R, Paradela A, Díez P, Dégano RM, Fuentes M, Orfao A, Montero AG, Garin-Muga A, Corrales FJ, Pino MMSD (2018). In-Depth Proteomic Characterization of Classical and Non-Classical Monocyte Subsets. Proteomes 6, E8.
Zagorac I, Fernandez-Gaitero S, Penning R, Post H, Bueno MJ, Mouron S, Manso L, Morente MM, Alonso S, Serra V, Muñoz J, Gómez-López G, Lopez-Acosta JF, Jimenez-Renard V, Gris-Oliver A, Al-Shahrour F, Piñeiro-Yañez E, Montoya-Suarez JL, Apala JV, Moreno-Torres A, Colomer R, Dopazo A, Heck AJR, Altelaar M, Quintela-Fandino M (2018). In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun 9, 3501.
Hurtado B, Trakala M, Ximénez-Embún P, El-Bakkali A, Partida D, Sanz-Castillo B, Álvarez-Fernández M, Maroto M, Sánchez-Martínez R, Martínez L, Muñoz J, García de Frutos P, Malumbres M (2018). Thrombocytopenia-associated mutations in Ser/Thr kinase MASTL deregulate actin cytoskeleton dynamics in platelets. J Clin Invest 128, 5351-5367.
Lynch CJ, Bernad R, Calvo I, Nóbrega-Pereira S, Ruiz S, Ibarz N, Martinez-Val A, Graña-Castro O, Gómez-López G, Andrés-León E, Espinosa Angarica V, Del Sol A, Ortega S, Fernandez-Capetillo O, Rojo E, Munoz J, Serrano M (2018). The RNA Polymerase II Factor RPAP1 Is Critical for Mediator-Driven Transcription and Cell Identity. Cell Reports 22, 396-410.
Priego N, Zhu L, Monteiro C, Mulders M, Wasilewski D, Bindeman W, Doglio L, Martínez L, Martínez-Saez E, Cajal SRY, Megías D, Hernández-Encinas E, Blanco-Aparicio C, Martínez L, Zarzuela E, Muñoz J, Fustero-Torres C, Pineiro E, Hernández-Laín A, Bertero L, Poli V, Sánchez-Martínez M, Menendez JA, Soffietti R, Bosch-Barrera J, Valiente M (2018). STAT3 labels a subpopulation of reactive astrocytes required for brain metastasis. Nat Med 24, 1024-1035.
Olmeda D, Cerezo-Wallis D, Riveiro-Falkenbach E, Pennacchi PC, Contreras-Alcalde M, Ibarz N, Cifdaloz M, Catena X, Calvo TG, Cañón E, Alonso-Curbelo D, Suarez J, Osterloh L, Graña O, Mulero F, Megías D, Cañamero M, Martínez-Torrecuadrada JL, Mondal C, Di Martino J, Lora D, Martinez-Corral I, Bravo-Cordero JJ, Muñoz J, Puig S, Ortiz-Romero P, Rodriguez-Peralto JL, Ortega S, Soengas MS (2017). Whole-body imaging of lymphovascular niches identifies pre-metastatic roles of midkine.. Nature 546, 676-680.
Zabala-Letona A, Arruabarrena-Aristorena A, Martín-Martín N, Fernandez-Ruiz S, Sutherland JD, Clasquin M, Tomas-Cortazar J, Jimenez J, Torres I, Quang P, Ximenez-Embun P, Bago R, Ugalde-Olano A, Loizaga-Iriarte A, Lacasa-Viscasillas I, Unda M, Torrano V, Cabrera D, van Liempd SM, Cendon Y, Castro E, Murray S, Revandkar A, Alimonti A, Zhang Y, Barnett A, Lein G, Pirman D, Cortazar AR, Arreal L, Prudkin L, Astobiza I, Valcarcel-Jimenez L, Zuñiga-García P, Fernandez-Dominguez I, Piva M, Caro-Maldonado A, Sánchez-Mosquera P, Castillo-Martín M, Serra V, Beraza N, Gentilella A, Thomas G, Azkargorta M, Elortza F, Farràs R, Olmos D, Efeyan A, Anguita J, Muñoz J, Falcón-Pérez JM, Barrio R, Macarulla T, Mato JM, Martinez-Chantar ML, Cordon-Cardo C, Aransay AM, Marks K, Baselga J, Tabernero J, Nuciforo P, Manning BD, Marjon K, Carracedo A (2017). mTORC1-dependent AMD1 regulation sustains polyamine metabolism in prostate cancer.. Nature 547, 109-113.
Rio-Machin A, Gómez-López G, Muñoz J, Garcia-Martinez F, Maiques-Diaz A, Alvarez S, Salgado RN, Shrestha M, Torres-Ruiz R, Haferlach C, Larráyoz MJ, Calasanz MJ, Fitzgibbon J, Cigudosa JC (2017). The molecular pathogenesis of the NUP98-HOXA9 fusion protein in acute myeloid leukemia.. Leukemia 31, 2000-2005.
Martinez-Val A, Garcia F, Ximénez-Embún P, Martínez Teresa-Calleja A, Ibarz N, Ruppen I, Munoz J (2017). Urea Artifacts Interfere with Immuno-Purification of Lysine Acetylation.. J Proteome Res 16, 1061-1068.
Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N1, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MM, Sancho J, Santamaría E, Vazquez J, Vilaseca M1 Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A (2017). A multicentric study to evaluate the use of relative retention times in targeted proteomics.. J Proteomics 152, 138-149.
Lecona E, Rodriguez-Acebes S, Specks J, Lopez-Contreras AJ, Ruppen I, Murga M, Muñoz J, Mendez J, Fernandez-Capetillo O (2016). USP7 is a SUMO deubiquitinase essential for DNA replication.. Nat Struct Mol Biol 23, 270-277.
Navarro P, Bueno MJ, Zagorac I, Mondejar T, Sanchez J, Mourón S, Muñoz J, Gómez-López G, Jimenez-Renard V, Mulero F, Chandel NS, Quintela-Fandino M (2016). Targeting Tumor Mitochondrial Metabolism Overcomes Resistance to Antiangiogenics.. Cell Reports 15, 2705-2718.
Martinez-Val A, Garcia F, Ximénez-Embún P, Ibarz N, Zarzuela E, Ruppen I, Mohammed S, Munoz J (2016). On the Statistical Significance of Compressed Ratios in Isobaric Labeling: A Cross-Platform Comparison.. J Proteome Res 15, 3029-3038.
Shakiba N, White CA, Lipsitz YY, Yachie-Kinoshita A, Tonge PD, Hussein SM, Puri MC, Elbaz J, Morrissey-Scoot J, Li M, Munoz J, Benevento M, Rogers IM, Hanna JH, Heck AJ, Wollscheid B, Nagy A, Zandstra PW (2015). CD24 tracks divergent pluripotent states in mouse and human cells.. Nat Communications 6, 7329.
The I, Ruijtenberg S, Bouchet BP, Cristobal A, Prinsen MB, van Mourik T, Koreth J, Xu H, Heck AJ, Akhmanova A, Cuppen E, Boxem M, Muñoz J, van den Heuvel S (2015). Rb and FZR1/Cdh1 determine CDK4/6-cyclin D requirement in C. elegans and human cancer cells. Nat Communications 6, 5906.
Wurm S, Zhang J, Guinea-Viniegra J, García F, Muñoz J, Bakiri L, Ezhkova E, Wagner EF (2015). Terminal epidermal differentiation is regulated by the interaction of Fra-2/AP-1 with Ezh2 and ERK1/2.. Genes Dev 29, 144-156.
Welling M, Chen HH, Muñoz J, Musheev MU, Kester L, Junker JP, Mischerikow N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, Heck AJ, Geijsen N (2015). DAZL regulates Tet1 translation in murine embryonic stem cells.. EMBO Rep 16, 791-802.
Chen HH, Welling M, Bloch DB, Muñoz J, Mientjes E, Chen X, Tramp C, Wu J, Yabuuchi A, Chou YF, Buecker C, Krainer A, Willemsen R, Heck AJ, Geijsen N (2015). DAZL Limits Pluripotency, Differentiation, and Apoptosis in Developing Primordial Germ Cells.. Stem Cell Reports 3, 892-904.
Benevento M, Tonge PD, Puri MC, Nagy A, Heck AJ, Munoz J (2015). Fluctuations in histone H4 isoforms during cellular reprogramming monitored by middle-down proteomics.. Proteomics (in press).
Hussein SM, Puri MC, Tonge PD, Benevento M, Corso AJ, Clancy JL, Mosbergen R, Li M, Lee DS, Cloonan N, Wood DL, Munoz J, Middleton R, Korn O, Patel HR, White CA, Shin JY, Gauthier ME, Lê Cao KA, Kim JI, Mar JC1 Shakiba N, Ritchie W, Rasko JE1, Grimmond SM, Zandstra PW, Wells CA, Preiss T, Seo JS, Heck AJ, Rogers IM, Nagy A (2014). Genome-wide characterization of the routes to pluripotency.. Nature 516, 198-206.
Tummala KS, Gomes AL, Yilmaz , Graña O, Bakiri L, Ruppen I, Ximénez-Embún P, Sheshappanavar V, Rodriguez-Justo M, Pisano DG, Wagner EF, Djouder N (2014). Inhibition of De Novo NAD+ Synthesis by Oncogenic URI Causes Liver Tumorigenesis through DNA Damage.. Cancer Cell 26, 826-839.
Benevento M, Tonge PD, Puri MC, Hussein SM, Cloonan N, Wood DL, Grimmond SM, Nagy A, Munoz J, Heck AJ (2014). Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks.. Nat Communications 5, 5613.
Clancy JL, Patel HR, Hussein SM, Tonge PD, Cloonan N, Corso AJ, Li M, Lee DS, Shin JY, Wong JJ, Bailey CG, Benevento M, Munoz J, Chuah A, Wood D, Rasko JE, Heck AJ, Grimmond SM, Rogers IM, Seo JS, Wells CA, Puri MC, Nagy A, Preiss T (2014). Small RNA changes en route to distinct cellular states of induced pluripotency.. Nat Communications 5, 5522.
Muñoz J, Heck AJ (2014). From the Human Genome to the Human Proteome.. Angewandte Chemie 53, 10864-10866.
Eguren M, Álvarez-Fernández M, García F, López-Contreras AJ, Fujimitsu K, Yaguchi H, Luque-García JL, Fernández-Capetillo O, Muñoz J, Yamano H, Malumbres M (2014). A synthetic lethal interaction between APC/C and topoisomerase poisons uncovered by proteomic screens.. Cell Reports 6, 670-683.
Saucedo-Cuevas LP, Ruppen I, Ximénez-Embún P, Domingo S, Gayarre J, Muñoz J, Silva JM, García MJ, Benítez J (2014). CUL4A contributes to the biology of basal-like breast tumors through modulation of cell growth and antitumor immune response.. Oncotarget 5, 2330-2343.
Altelaar AF, Munoz J, Heck AJ (2013). Next-generation proteomics: towards an integrative view of proteome dynamics.. Nat Rev Genet 14, 35-48.
Schonthaler HB, Guinea-Viniegra J, Wculek SK, Ruppen I, Ximénez-Embún P, Guío-Carrión A, Navarro R, Hogg N, Ashman K, Wagner EF (2013). S100A8/A9 (calprotectin) is a mediator in psoriasis controlling expression of complement factor C3.. Immunity 39, 1171-1181.
López-Contreras AJ, Ruppen I, Nieto-Soler M, Murga M, Rodriguez- Acebes S, Remeseiro S, Rodrigo-Perez S, Rojas AM, Mendez J, Muñoz J, Fernandez-Capetillo O (2013). A proteomic characterization of factors enriched at nascent DNA molecules.. Cell Reports 3, 1-12.
Martínez P, Gómez-López G, García F, Mercken E, Mitchell S, Flores JM, De Cabo R, Blasco MA (2013). RAP1 protects from obesity through its extratelomeric role regulating gene expression.. Cell Reports 3, 2059-2074.
de Cubas AA, Leandro-Garcia LJ, Schiavi F, Mancikova V, Comino-Méndez I, Inglada-Perez L, Pérez M, Ibarz N, Ximénez-Embún P, López-Jiménez E, Letón R, Maliszewska A, Gómez Graña A, Bernal C, Alvarez-Escolá C, Rodriguez-Antona C, Opocher G, Muñoz J, Megías D, Cascón A, Robledo M (2013). Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways.. Endocr-Relat Cancer 20, 477-493.
Berends CW, Muñoz J, Portegijs V, Schmidt R, Grigoriev I, Boxem M, Akhmanova A, Heck AJ, van den Heuvel S (2013). F-actin asymmetry and the endoplasmic reticulum-associated TCC-1 protein contribute to stereotypic spindle movements in the Caenorhabditis elegans embryo.. Mol Biol Cell 24, 2201-2215.
Di Palma S, Zoumaro-Djayoon A, Peng M, Post H, Preisinger C, Munoz J, Heck AJ (2013). Finding the same needles in the haystack? A comparison of phosphotyrosine peptides enriched by immuno-affinity precipitation and metal-based affinity chromatography.. J Proteomics 91, 331-337.
Gámez-Pozo A, Ferrer NI, Ciruelos E, López-Vacas R, Martínez FG, Espinosa E, Vara JA (2013). Shotgun proteomics of archival triple-negative breast cancer samples.. Proteomics Clinical Applications 7, 283-291.