C-terminal sequences in R-Ras are involved in integrin regulation and in plasma membrane microdomain distribution

The small GTPases R-Ras and H-Ras are highly homologous proteins with contrasting biological properties, for example, they differentially modulate integrin affinity: H-Ras suppresses integrin activation in fibroblasts whereas R-Ras can reverse this effect of H-Ras. To gain insight into the sequences directing this divergent phenotype, we investigated a panel of H-Ras/R-Ras chimeras and found that sequences in the R-Ras hypervariable C-terminal region including amino acids 175-203 are required for the R-Ras ability to increase integrin activation in CHO cells; however, the proline-rich site in this region, previously reported to bind the adaptor protein Nck, was not essential for this effect. In addition, we found that the GTPase TC21 behaved similarly to R-Ras. Because the C-termini of Ras proteins can control their subcellular localization, we compared the localization of H-Ras and R-Ras. In contrast to H-Ras, which migrates out of lipid rafts upon activation, we found that activated R-Ras remained localized to lipid rafts. However, functionally distinct H-Ras/R-Ras chimeras containing different C-terminal R-Ras segments localized to lipid rafts irrespective of their integrin phenotype. (C) 2003 Elsevier Inc. All rights reserved.

Detection of codon 12 mutation in the k-ras oncogene in pancreatic tumors

Mutations at codons 12, 13, or 61 of the H-ras, K-ras, and N-ras have been detected in human neoplasias by a variety of techniques. Some of these techniques are very sensitive and can detect K-ras mutation in 90% of the cases of pancreatic adenocarcinomas. We analyzed 11 samples of pancreatic adenocarcinoma, three samples of pancreatic mucinous cystadenoma, and two samples without tumors in formalin-fixed paraffin embedded tissue sections. K-ras mutations at codon 12 were detected by a two-step PCR-enriched technique in all the samples of pancreatic adenocarcinoma, but not in cystadenoma or control samples. This technique may be useful for early detection of pancreatic cancer.

Anàlisi de l'expressió de gens de proteïnes de cohesió cromosòmica en oòcits humans

Projecte de recerca elaborat a partir d’una estada al Mount Sinai School Mountain, Estats Units, entre abril i juliol del 2007. Les aneuploïdies cromosòmiques en humans constitueixen un problema genètic amb gran repercussió clínica i social. Afecten un 5% dels embarassos reconeguts clínicament i la seva incidència augmenta amb l’edat materna Les aneuploïdies estan íntimament lligades al procés d’oogènesi, que ha demostrat ser un procés que tendeix encara més a l’error a mesura que la dona envelleix. Estudis recents realitzats en ratolí han demostrat que la deficiència d’una proteïna de cohesió cromosòmica (SMC1b) provoca l’aparició d’aneuploïdies i que augmenta amb l’edat, similarment a la situació en la dona. Fins al moment, però, no hi ha estudis al respecte en l’espècie humana. Durant l’estada es va posar a punt una metodologia per analitzar l’expressió de SMC1b en oòcits humans, amb la finalitat de demostrar si la seva expressió disminueix a mesura que la dona envelleix, i pot explicar l’efecte de l’edat materna sobre la taxa d’aneuploïdies.

Organització nuclear dels gens que codifiquen per a les proteïnes làcties en cèlules epitelials mamàries en diferents estadis de desenvolupament

Estudi realitzat a partir d’una estada al Institut National de la Recherche Agronomique (INRA), a França, entre 2006 i 2008. En el ultims anys, estudis realitzats en diferents tipus cel•lulars han pogut determinar l’importància de l’organització nuclear en el control i regulació gènica. S’han realizat diferents experiments per tal de determinar si la posició dels gens de les proteïnes làcties en el nucli interfàsic de cel•lules epitelials mamaries és important per regular la seva expressió. Els gens de les proteïnes de la llet s’expressen a la glàndula mamaria durant la lactació en resposta a les hormones lactogèniques (majoritàriament prolactina i glucocorticoids). Mitjançant la tècnica de FISH (fluorescent in situ hibridization) en 3D s’ha caracteritzat la localització nuclear del gens WAP (whey acidic protein) i les caseïnes en cèl•lules epitelials mamaries de ratolí (HC11) cultivades en l’absència i presencia d’hormones lactogèniques. En absència d’hormones, els dos gens estan distribuïts dins del nucli de forma no aleatòria, el gen WAP es troba localitzat en l’interior del nucli, mentre que les caseïnes es troben localitzades prop de la perifèria nuclear. L’estimulació hormonal indueix un canvi significatiu en la distància dels dos gens a la perifèria nuclear. Així mateix, la posició del locus de la caseïna en relació al seu territori cromosòmic (CT) 5 està correlacionada amb la inducció hormonal i per tant amb la seva activació transcripcional, mentre que la posició del gen WAP amb relació al seu CT11 sembla més determinada pel context cromosòmic del gen. Per últim, no s’han trobat diferencies en la localització dels gens en relació a l'heterocromatina del centròmer, descrit com a compartiment repressiu, entre les cèl•lules estimulades amb hormones i les que no. En els dos casos s’ha trobat un gran percentatge de gens que no estan associats als centròmers.

Combinatorial Synthesis and Biological Evaluation of Inhibitors of D-Ala-D-Ala-Ligase

Report for the scientific sojourn carried out at the Max Planck Institut of Molecular Phisiology, Germany, from 2006 to 2008.The work carried out during this postdoctoral stage was focused on two different projects. Firstly, identification of D-Ala D-Ala Inhibitors and the development of new synthethic approaches to obtain lipidated peptides and proteins and the use of these lipidated proteins in biological and biophysical studies. In the first project, new D-Ala D-Ala inhibitors were identified by using structural alignments of the ATP binding sites of the bacterial ligase DDl and protein and lipid kinases in complex with ATP analogs. We tested a series of commercially available kinase inhibitors and found LFM-A13 and Tyrphostine derivatives to inhibit DDl enzyme activity. Based on the initial screening results we synthesized a series of malononitrilamide and salicylamide derivatives and were able to confirm the validity of these scaffolds as inhibitors of DDl. From this investigation we gained a better understanding of the structural requirements and limitations necessary for the preparation of ATP competitive DDl inhibitors. The compounds in this study may serve as starting points for the development of bi-substrate inhibitors that incorporate both, an ATP competitive and a substrate competitive moiety. Bisubstrate inhibitors that block the ATP and D-Ala binding sites should exhibit enhanced selectivity and potency profiles by preferentially inhibiting DDl over kinases. In the second project, an optimized synthesis for tha alkylation of cysteins using the thiol ene reaction was establisehd. This new protocol allowed us to obtain large amounts of hexadecylated cysteine that was required for the synthesis of differently lipidated peptides. Afterwards the synthesis of various N-ras peptides bearing different lipid anchors was performed and the peptides were ligated to a truncated N-ras protein. The influence of this differently lipidated N-ras proteins on the partioning and association of N-Ras in model membrane subdomains was studied using Atomic Force Microscopy.

The type of K-ras mutation determines prognosis in colorectal cancer.

BACKGROUND: Mutations involving the oncogene K-ras in colorectal cancer may be related to tumor aggressiveness. However, the value of K-ras gene determination as a prognostic marker has not been clearly established. PATIENTS AND METHODS: The results from 98 patients recruited in a prospective study analyzing the effect of a K-ras mutation as a prognostic factor in colorectal cancer are reported. RESULTS: Disease-free (P = 0.02) and overall survival (P = 0.03) were significantly reduced for patients harboring a K-ras mutation. Two specific mutations demonstrated a significantly increased risk of disease recurrence, namely, 12-TGT (P = 0.04) and 13-GAC substitutions (P = 0.002). Patients with either of these substitutions had a 2-year disease-free survival rate of 37% compared with that of 67% for the group of patients harboring any other mutation type or a wild-type status (P = 0.01). CONCLUSIONS: The results herein presented suggest that K-ras acts as a prognostic factor in colorectal cancer and that this effect is probably related to a limited number of defined mutations.

Oncogenic Ras inhibits Fas ligand-mediated apoptosis by downregulating the expression of Fas.

Tumor growth is the result of deregulated tissue homeostasis which is maintained through the delicate balance of cell growth and apoptosis. One of the most efficient inducers of apoptosis is the death receptor Fas. We report here that oncogenic Ras (H-Ras) downregulates Fas expression and renders cells of fibroblastic and epitheloid origin resistant to Fas ligand-induced apoptosis. In Ras-transformed cells, Fas mRNA is absent. Inhibition of DNA methylation restores Fas expression. H-Ras signals via the PI 3-kinase pathway to downregulate Fas, suggesting that the known anti-apoptotic effect of the downstream PKB/Akt kinase may be mediated, at least in part, by the repression of Fas expression. Thus, the oncogenic potential of H-ras may reside on its capacity not only to promote cellular proliferation, but also to simultaneously inhibit Fas-triggered apoptosis.

Síntesi de siRNAs (short interfering RNAs) modificats amb nucleobases 5-metil i 5-propinil pirimidíniques i avaluació de la seva activitat in vitro en cultius cel•lulars i de la seva estabilitat en sèrum humà. Disseny de siRNAs dirigits a la inhibició de l'expressió de mutacions de l'oncogen K-ras.

Projecte de recerca elaborat a partir d’una estada a la Stanford University, EEUU, entre 2007 i 2009. El present projecte es basa 1) en la síntesi de cadenes d'ARN dirigides a la inhibició de l'expressió gènica per un mecanisme d'ARN d'interferència (siRNAs o short interefering RNAs) i 2) en l'avaluació de l'activitat in vitro d'aquests oligonucleòtids en cultius cel•lulars. Concretament, la meva recerca ha estat enfocada principalment a l'estudi de cadenes de siRNA modificades amb nucleobases 5-metil i 5-propinil pirimidíniques. Es tractava d'avaluar l'efecte que exerceixen els factors estèrics en el major groove (solc major) dels siRNAs sobre la seva activitat biològica. En aquest sentit, he dut aterme síntesi de fosforamidits de nucleòsis pirimidínics modificats a la posició C-5 de la nucleobase. A continuació he incorporat aquestes unitats nucleosídiques en cadenes d'ARN emprant un sintetitzador d’ADN/ARN i he estudiat l'estabilitat dels corresponents dúplexs d'ARN mitjançant experiments de desnaturalització tèrmica. Finalment he dut a terme experiments d'inhibició de l'expressió gènica en cèl.lules HeLa per tal d'avaluar l'activitat biològia d'aquests siRNAs modificats. Els resultats d'aquests estudis han posat de manifest que la presència de grups voluminosos com el propinil a l'extrem 5' del dúplex de siRNA (definit per la cadena guia o antisense) influeix de forma molt negativa en la seva activitat biològica. En canvi, grups menys voluminosos com el metil hi influeixen positivament, de manera que algunes de les cadenes sintetitzades han resultat ser més actives que els corresponents siRNAs naturals (wild type siRNAs). A més, aquest tipus de modificació contribueix positivament en l'estabilitat de cadenes de siRNA en sèrum humà. Aquest treball ha estat publicat (Terrazas, M.; Kool, E.T. "Major Groove Modifications Improve siRNA Stability and Biological Activity" Nucleic Acids Res. 2009, in press).

Estudi de la relació estructura-funció de les proteïnes CPT1

En aquest treball s’ha analitzat la relació estructura-funció dels enzims CPT1, o Carnitina palmitoïltransferasa 1, que catalitza la reacció de transesterificació dels àcids grassos de cadena llarga a acil-carnitines, per tal que puguin accedir a la matriu mitocondrial i ser oxidats. Aquest enzim es troba estrictament regulat per malonil-CoA, primer intermediari de la síntesi d’àcids grassos, establint-se així una regulació coordinada entre la formació i la degradació de grasses. S’han estudiat els tres isotips de CPT1 descrits fins al moment: CPT1A, CPT1B i CPT1C. Mitjançant l’expressió heteròloga de mutants de CPT1A de rata i CPT1B de porc en el llevat P. pastoris, s’ha estudiat l’efecte sobre la inhibició per malonil-CoA de petits canvis en la seva estructura, per tal de trobar una relació entre la seva funció enzimàtica i la disposició conformacional de la proteïna. Segons els resultats obtinguts, el residu Glu590 de CPT1A de rata estaria impedint la unió de l’inhibidor, mentre que el residu Met593 estaria afavorint aquesta unió. Els estudis amb l’enzim CPT1B de porc demostraren l’existència d’un determinant positiu per la sensibilitat al malonil-CoA en els primers 18 residus de la proteïna, i definiren la posició Glu17 com la responsable de l’alta afinitat a la carnitina i la baixa sensibilitat a la inhibició per malonil-CoA (8). Es clonà i caracteritzà la regió promotora del gen de CPT1C humana, amb la intenció d’analitzar la funcionalitat de putatius elements de resposta identificats in silico. Cap dels elements estudiats resultà ser funcional in vivo. A més, es demostrà que la manca d’activitat catalítica de la proteïna no és deguda a l’extensió C-terminal que presenta respecte els isotips A i B, tot i presentar un alt percentatge d’identitat de seqüència. S’ha amplificat una isoforma humana de CPT1C (Pubmed Acc. Num. AK299866), corresponent a la regió carboxiterminal de la proteïna, que es pretén utilitzar per obtenir el primer cristall de la part soluble d’una proteïna CPT1.     

LDLs stimulate p38 MAPKs and wound healing through SR-BI independently of Ras and PI3 kinase.

Intracellular signals elicited by LDLs are likely to play a role in the pathogenesis associated with increased LDL blood levels. We have previously determined that LDL stimulation of human skin fibroblasts, used as a model system for adventitial fibroblasts, activates p38 mitogen-activated protein kinases (MAPKs), followed by IL-8 production and increased wound-healing capacity of the cells. The proximal events triggering these responses had not been characterized, however. Here we show that MAPK kinases MKK3 and MKK6, but not MKK4, are the upstream kinases responsible for the activation of the p38 MAPKs and stimulation of wound closure in response to LDLs. Phosphoinositide 3 kinases (PI3Ks) and Ras have been suggested to participate in lipoprotein-induced MAPK activation. However, specific PI3K inhibitors or expression of a dominant-negative form of Ras failed to blunt LDL-induced p38 MAPK activation. The classical LDL receptor does not participate in LDL signaling, but the contribution of other candidate lipoprotein receptors has not been investigated. Using cells derived from scavenger receptor class B type I (SR-BI) knockout mice or the BLT-1 SR-BI inhibitor, we now show that this receptor is required for LDLs to stimulate p38 MAPKs and to promote wound healing. Identification of MKK3/6 and SR-BI as cellular relays in LDL-mediated p38 activation further defines the signaling events that could participate in LDL-mediated pathophysiological responses.

Regression of cardiac growth in kidney transplant recipients using anti-m-TOR drugs plus RAS blockers: a controlled longitudinal study.

BACKGROUND Left ventricular hypertrophy (LVH) is common in kidney transplant (KT) recipients. LVH is associated with a worse outcome, though m-TOR therapy may help to revert this complication. We therefore conducted a longitudinal study to assess morphological and functional echocardiographic changes after conversion from CNI to m-TOR inhibitor drugs in nondiabetic KT patients who had previously received RAS blockers during the follow-up. METHODS We undertook a 1-year nonrandomized controlled study in 30 non-diabetic KT patients who were converted from calcineurin inhibitor (CNI) to m-TOR therapy. A control group received immunosuppressive therapy based on CNIs. Two echocardiograms were done during the follow-up. RESULTS Nineteen patients were switched to SRL and 11 to EVL. The m-TOR group showed a significant reduction in LVMi after 1 year (from 62 ± 22 to 55 ± 20 g/m2.7; P=0.003, paired t-test). A higher proportion of patients showing LVMi reduction was observed in the m-TOR group (53.3 versus 29.3%, P=0.048) at the study end. In addition, only 56% of the m-TOR patients had LVH at the study end compared to 77% of the control group (P=0.047). A significant change from baseline in deceleration time in early diastole was observed in the m-TOR group compared with the control group (P=0.019). CONCLUSIONS Switching from CNI to m-TOR therapy in non-diabetic KT patients may regress LVH, independently of blood pressure changes and follow-up time. This suggests a direct non-hemodynamic effect of m-TOR drugs on cardiac mass.

FGF signaling controls caudal hindbrain specification through Ras-ERK1/2 pathway

Background: During early steps of embryonic development the hindbrain undergoes a regionalization process along the anterior-posterior (AP) axis that leads to a metameric organization in a series of rhombomeres (r). Refinement of the AP identities within the hindbrain requires the establishment of local signaling centers, which emit signals that pattern territories in their vicinity. Previous results demonstrated that the transcription factor vHnf1 confers caudal identity to the hindbrain inducing Krox20 in r5 and MafB/Kreisler in r5 and r6, through FGF signaling [1].Results: We show that in the chick hindbrain, Fgf3 is transcriptionally activated as early as 30 min after mvHnf1 electroporation, suggesting that it is a direct target of this transcription factor. We also analyzed the expression profiles of FGF activity readouts, such as MKP3 and Pea3, and showed that both are expressed within the hindbrain at early stages of embryonic development. In addition, MKP3 is induced upon overexpression of mFgf3 or mvHnf1 in the hindbrain, confirming vHnf1 is upstream FGF signaling. Finally, we addressed the question of which of the FGF-responding intracellular pathways were active and involved in the regulation of Krox20 and MafB in the hindbrain. While Ras-ERK1/2 activity is necessary for MKP3, Krox20 and MafB induction, PI3K-Akt is not involved in that process.Conclusion: Based on these observations we propose that vHnf1 acts directly through FGF3, and promotes caudal hindbrain identity by activating MafB and Krox20 via the Ras-ERK1/2 intracellular pathway.

Estudi de la interacció de tres complexos de Pt amb proteïnes i oligonucleòtids mitjançant ESI-MS

En aquest treball s’investiga la reactivitat de tres complexos de Pt, cisplatí, complex 1, [Pt(dmba)(aza-N1)(dmso)], complex 2, i [Pt(dmba)(N9-9AA)(PPh3)]+, complex 3; els quals presenten activitat antitumoral, amb diferents proteïnes i oligonucleòtids mitjançant espectrometria de masses (ESI-TOF MS). ). L’estudi del cisplatí, 1, droga molt coneguda i emprada avui en dia pel tractament de molts tipus de càncer, permet comparar la reactivitat dels nous complexos d’estudi, 2 i 3, els quals presenten un IC50 més baix que el cisplatí en algunes línies de cèl·lules tumorals.

Inhibition of Mitogen-Activated Protein Kinase Erk1/2 Promotes Protein Degradation of ATP Binding Cassette Transporters A1 and G1 in CHO and in HuH7 cells.

Signal transduction modulates expression and activity of cholesterol transporters. We recently demonstrated that the Ras/mitogen-activated protein kinase (MAPK) signaling cascade regulates protein stability of Scavenger Receptor BI (SR-BI) through Proliferator Activator Receptor (PPARα) -dependent degradation pathways. In addition, MAPK (Mek/Erk 1/2) inhibition has been shown to influence liver X receptor (LXR) -inducible ATP Binding Cassette (ABC) transporter ABCA1 expression in macrophages. Here we investigated if Ras/MAPK signaling could alter expression and activity of ABCA1 and ABCG1 in steroidogenic and hepatic cell lines. We demonstrate that in Chinese Hamster Ovary (CHO) cells and human hepatic HuH7 cells, extracellular signal-regulated kinase 1/2 (Erk1/2) inhibition reduces PPARα-inducible ABCA1 protein levels, while ectopic expression of constitutively active H-Ras, K-Ras and MAPK/Erk kinase 1 (Mek1) increases ABCA1 protein expression, respectively. Furthermore, Mek1/2 inhibitors reduce ABCG1 protein levels in ABCG1 overexpressing CHO cells (CHO-ABCG1) and human embryonic kidney 293 (HEK293) cells treated with LXR agonist. This correlates with Mek1/2 inhibition reducing ABCG1 cell surface expression and decreasing cholesterol efflux onto High Density Lipoproteins (HDL). Real Time reverse transcriptase polymerase chain reaction (RT-PCR) and protein turnover studies reveal that Mek1/2 inhibitors do not target transcriptional regulation of ABCA1 and ABCG1, but promote ABCA1 and ABCG1 protein degradation in HuH7 and CHO cells, respectively. In line with published data from mouse macrophages, blocking Mek1/2 activity upregulates ABCA1 and ABCG1 protein levels in human THP1 macrophages, indicating opposite roles for the Ras/MAPK pathway in the regulation of ABC transporter activity in macrophages compared to steroidogenic and hepatic cell types. In summary, this study suggests that Ras/MAPK signaling modulates PPARα- and LXR-dependent protein degradation pathways in a cell-specific manner to regulate the expression levels of ABCA1 and ABCG1 transporters.

Calcineurin inhibitors activate the proto-oncogene Ras and promote protumorigenic signals in renal cancer cells.

The development of cancer is a major problem in immunosuppressed patients, particularly after solid organ transplantation. We have recently shown that calcineurin inhibitors (CNI) used to treat transplant patients may play a critical role in the rapid progression of renal cancer. To examine the intracellular signaling events for CNI-mediated direct tumorigenic pathway(s), we studied the effect of CNI on the activation of proto-oncogenic Ras in human normal renal epithelial cells (REC) and renal cancer cells (786-0 and Caki-1). We found that CNI treatment significantly increased the level of activated GTP-bound form of Ras in these cells. In addition, CNI induced the association of Ras with one of its effector molecules, Raf, but not with Rho and phosphatidylinositol 3-kinase; CNI treatment also promoted the phosphorylation of the Raf kinase inhibitory protein and the downregulation of carabin, all of which may lead to the activation of the Ras-Raf pathway. Blockade of this pathway through either pharmacologic inhibitors or gene-specific small interfering RNA significantly inhibited CNI-mediated augmented proliferation of renal cancer cells. Finally, it was observed that CNI treatment increased the growth of human renal tumors in vivo, and the Ras-Raf pathway is significantly activated in the tumor tissues of CNI-treated mice. Together, targeting the Ras-Raf pathway may prevent the development/progression of renal cancer in CNI-treated patients.