2021

Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq data.

Fustero-Torre C, Jiménez-Santos MJ, García-Martín S, Carretero-Puche C, García-Jimeno L, Ivanchuk V, Di Domenico T, Gómez-López G, Al-Shahrour F.
Genome Med. 2021 Dec 16;13(1):187. doi: 10.1186/s13073-021-01001-x.
PMID: 34911571

Melanoma-derived small extracellular vesicles induce lymphangiogenesis and metastasis through an NGFR-dependent mechanism.

García-Silva, S., Benito-Martín, A., Graña-Castro O., Nogués, L. et al.
Nat Cancer. 2021 Nov 25. doi: 10.1038/s43018-021-00272-y
PMID: 34957415

APPRIS: selecting functionally important isoforms.

Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML.
Nucleic Acids Res. 2021 Nov 10. doi: 10.1093/nar/gkab1058. Online ahead of print.
PMID: 34755885

IL-1 Mediates Microbiome-Induced Inflamm-Ageing of Hematopoietic Stem Cells in Mice.

Kovtonyuk LV, Caiado F, Garcia-Martin S, Manz EM, Helbling PM, Takizawa H, Boettcher S, Al-Shahrour F, Nombela-Arrieta C, Slack E, Manz MG.
Blood. 2021 Sep 15. doi: 10.1182/blood.2021011570. Epub ahead of print.
PMID: 34525198

Deficient adaptation to centrosome duplication defects in neural progenitors causes microcephaly and subcortical heterotopias.

González-Martínez J, Cwetsch AW, Martínez-Alonso D, López-Sainz LR, Almagro J, Melati A, Gómez J, Pérez-Martínez M, Megías D, Boskovic J, Gilabert-Juan J, Graña-Castro O, Pierani A, Behrens A, Ortega S, Malumbres M.
JCI Insight. 2021 Aug 23;6(16):146364. doi: 10.1172/jci.insight.146364.
PMID: 34237032

The clinical importance of tandem exon duplication-derived substitutions.

Martinez-Gomez L, Pozo F, Walsh T.A, Abascal F, Tress M.L. Nucleic Acids Research 2021; doi: 10.1093/nar/gkab623
PMID: 34302486

Inhibition of Rag GTPase signaling in mice suppresses B cell responses and lymphomagenesis with minimal detrimental trade-offs.

Ortega-Molina A, Lebrero-Fernández C, Sanz A, Deleyto-Seldas N, Plata-Gómez A.B, Menéndez C, Graña-Castro O, Caleiras E, Efeyan A.
Cell Reports. 2021 Jul 13. doi: 10.1016/j.celrep.2021.109372.
PMID: 34260908

NKG2D-CAR-transduced natural killer cells efficiently target multiple myeloma.

Leivas A, Valeri A, Córdoba L, García-Ortiz A, Ortiz A, Sánchez-Vega L, Graña-Castro O, Fernández L, Carreño-Tarragona G, Pérez M, Megías D, Paciello ML, Sánchez-Pina J, Pérez-Martínez A, Lee DA, Powell DJ Jr, Río P, Martínez-López J.
Blood Cancer J. 2021 Aug 14;11(8):146. doi: 10.1038/s41408-021-00537-w.
PMID: 34392311

Inactivation of EMILIN-1 by Proteolysis and Secretion in Small Extracellular Vesicles Favors Melanoma Progression and Metastasis.

Amor López A, Mazariegos MS, Capuano A, Ximénez-Embún P, Hergueta-Redondo M, Recio JÁ, Muñoz E, Al-Shahrour F, Muñoz J, Megías D, Doliana R, Spessotto P, Peinado H.
Int J Mol Sci. 2021 Jul 9;22(14):7406. doi: 10.3390/ijms22147406.
PMID: 34299025

A comprehensive database for integrated analysis of omics data in autoimmune diseases.

Martorell-Marugán J, López-Domínguez R, García-Moreno A, Toro-Domínguez D, Villatoro-García JA, Barturen G, Martín-Gómez A, Troule K, Gómez-López G, Al-Shahrour F, González-Rumayor V, Peña-Chilet M, Dopazo J, Sáez-Rodríguez J, Alarcón-Riquelme ME, Carmona-Sáez P.
BMC Bioinformatics. 2021 Jun 24;22(1):343. doi: 10.1186/s12859-021-04268-4.
PMID: 34167460

MicroRNAs Targeting HIF-2α, VEGFR1 and/or VEGFR2 as Potential Predictive Biomarkers for VEGFR Tyrosine Kinase and HIF-2α Inhibitors in Metastatic Clear-Cell Renal Cell Carcinoma.

Kinget, L.; Roussel, E.; Verbiest, A.; Albersen, M.; Rodríguez-Antona, C.; Graña-Castro, O.; Inglada-Pérez, L.; Zucman-Rossi, J.; Couchy, G.; Job, S.; de Reyniès, A.; Laenen, A.; Baldewijns, M.; Beuselinck, B.
Cancers 2021, 13, 3099. doi: 10.3390/cancers13123099
PMID: 34205829

Compi: a framework for portable and reproducible pipelines.

López-Fernández H, Graña-Castro O, Nogueira-Rodríguez A, Reboiro-Jato M, Glez-Peña D.
PeerJ Computer Science. 2021 June 18; doi: 10.7717/peerj-cs.593
PMID: 34239974

Assessing the functional relevance of splice isoforms.

Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML.
NAR Genom Bioinform. 2021 May 22;3(2):lqab044. doi: 10.1093/nargab/lqab044.
PMID: 34046593

RANK links senescence to stemness in the mammary epithelia, delaying tumor onset but increasing tumor aggressiveness.

Benítez S, Cordero A, Santamaría G.P, Redondo-Pedraza J, Rocha S.A, Collado-Solé A, Jimenez M, Sanz-Moreno A, Yoldi G, Santos C. J, De Benedictis I, Gómez-Aleza C, Da Silva-Álvarez S, Troulé K, Gómez-López G, Alcazar N, Palmero I, Collado M, Serrano M, Gonzalez-Suarez E
Developmental Cell. 2021 May 17; doi:10.1016/j.devcel.2021.04.022.
PMID: 34004159

Dianhydrogalactitol Overcomes Multiple Temozolomide Resistance Mechanisms in Glioblastoma.

Jiménez-Alcázar M, Curiel-García Á, Nogales P, Perales-Patón J, Schuhmacher AJ, Galán-Ganga M, Zhu L, Lowe SW, Al-Shahrour F, Squatrito M.
Mol Cancer Ther. 2021 Jun;20(6):1029-1038. doi: 10.1158/1535-7163.MCT-20-0319. Epub 2021 Apr 12.
PMID: 33846235

MicroRNAs Possibly Involved in the Development of Bone Metastasis in Clear-Cell Renal Cell Carcinoma.

Kinget L, Roussel E, Lambrechts D, Boeckx B, Vanginderhuysen L, Albersen M, Rodríguez-Antona C, Graña-Castro O, Inglada-Pérez L, Verbiest A, Zucman-Rossi J, Couchy G, Caruso S, Laenen A, Baldewijns M, Beuselinck B.
Cancers (Basel). 2021 Mar 28;13(7):1554. doi: 10.3390/cancers13071554.
PMID: 33800656

Short and dysfunctional telomeres sensitize the kidneys to develop fibrosis.

Saraswati, S., Martínez, P., Graña-Castro, O. Blasco M.A.
Nat Aging 1, 269–283 (2021). doi: 10.1038/s43587-021-00040-8. 37118410

Association between BRCA2 alterations and intraductal and cribriform histologies in prostate cancer.

Lozano R, Salles D.C, Shahneen S, Aragón M.I, Thorne H, López-Campos F, Rubio-Briones J, Gutierrez-Pecharroman M.A, Maldonado L, Di Domenico T, Sanz A, Prieto J.D, García I, Pacheco I.M, Garcés T, Llacer C, Romero-Laorden N, Zambrana F, López-Casas P.P, Llorente D, Mateo J, Pritchard C.C, Antonarakis S.E, Olmos D, Lotan L.T, Castro E.
Eur. J. Cancer. 2021 Feb 21;147:74-83. doi: 10.1016/j.ejca.2021.01.027. Online ahead of print.
PMID: 33626496

GENCODE 2021.

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland E.J,Mudge J.M, Sisu C, Wright J.C, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes I.T, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier t, Howe K.L, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro C.P.F, Parker A, Pei V, Pozo F, Calvet Riera F, Ruffier M, Schmitt B.M, Stapleton E, Suner M-M, Sycheva I, Uszczynska-Ratajczak B, Wolf M.Y, Xu J, Yang Y.T, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard J.P. T, Kellis M, Paten B, Tress M.L, Flicek P.
Nucleic Acids Res, Volume 49, Issue D1, 8 January 2021, Pages D916–D923, doi: 10.1093/nar/gkaa1087
PMID: 33270111

CSVS, a crowdsourcing database of the Spanish population genetic variability.

Peña-Chilet M, Roldán G, Perez-Florido J, Ortuño FM, Carmona R, Aquino V, Lopez-Lopez D, Loucera C, Fernandez-Rueda JL, Gallego A, García-Garcia F, González-Neira A, Pita G, Núñez-Torres R, Santoyo-López J, Ayuso C, Minguez P, Avila-Fernandez A, Corton M, Moreno-Pelayo MÁ, Morin M, Gallego-Martinez A, Lopez-Escamez JA, Borrego S, Antiñolo G, Amigo J, Salgado-Garrido J, Pasalodos-Sanchez S, Morte B; Spanish Exome Crowdsourcing Consortium, Carracedo Á, Alonso Á, Dopazo J.
Nucleic Acids Res. 2021 Jan 8;49(D1):D1130-D1137. doi: 10.1093/nar/gkaa794.
PMID: 32990755

Spleen plays a major role in DLL4-driven acute T-cell lymphoblastic leukemia.

Xiong H, Mancini M, Gobert M, Shen S, Furtado GC, Lira SA, Parkhurst CN, Garambois V, Brengues M, Tadokoro CE, Trimarchi T, Gómez-López G, Singh A, Khiabanian H, Minuzzo S, Indraccolo S, Lobry C, Aifantis I, Herranz D, Lafaille JJ, Maraver A.
Theranostics. 2021 Jan 1;11(4):1594-1608. doi: 10.7150/thno.48067. eCollection 2021.
PMID: 33408769