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1.
Int J Mol Sci ; 25(18)2024 Sep 13.
Artículo en Inglés | MEDLINE | ID: mdl-39337373

RESUMEN

Microbiota and luminal components may affect epithelial integrity and thus participate in the pathophysiology of colon cancer (CC) and inflammatory bowel disease (IBD). Therefore, we aimed to determine the effects of fecal luminal factors derived from patients with CC and ulcerative colitis (UC) on the colonic epithelium using a standardized colon-derived two-dimensional epithelial monolayer. The complex primary human stem cell-derived intestinal epithelium model, termed RepliGut® Planar, was expanded and passaged in a two-dimensional culture which underwent stimulation for 48 h with fecal supernatants (FS) from CC patients (n = 6), UC patients with active disease (n = 6), and healthy subjects (HS) (n = 6). mRNA sequencing of monolayers was performed and cytokine secretion in the basolateral cell culture compartment was measured. The addition of fecal supernatants did not impair the integrity of the colon-derived epithelial monolayer. However, monolayers stimulated with fecal supernatants from CC patients and UC patients presented distinct gene expression patterns. Comparing UC vs. CC, 29 genes were downregulated and 33 genes were upregulated, for CC vs. HS, 17 genes were downregulated and five genes were upregulated, and for UC vs. HS, three genes were downregulated and one gene was upregulated. The addition of FS increased secretion of IL8 with no difference between the study groups. Fecal luminal factors from CC patients and UC patients induce distinct colonic epithelial gene expression patterns, potentially reflecting the disease pathophysiology. The culture of colonic epithelial monolayers with fecal supernatants derived from patients may facilitate the exploration of IBD- and CC-related intestinal microenvironmental and barrier interactions.


Asunto(s)
Colitis Ulcerosa , Neoplasias del Colon , Heces , Mucosa Intestinal , Humanos , Colitis Ulcerosa/genética , Colitis Ulcerosa/metabolismo , Colitis Ulcerosa/patología , Heces/microbiología , Mucosa Intestinal/metabolismo , Neoplasias del Colon/genética , Neoplasias del Colon/metabolismo , Neoplasias del Colon/patología , Femenino , Masculino , Colon/metabolismo , Colon/patología , Células Epiteliales/metabolismo , Persona de Mediana Edad , Adulto , Citocinas/metabolismo , Células Cultivadas , Anciano
2.
EMBO J ; 38(23): e101323, 2019 12 02.
Artículo en Inglés | MEDLINE | ID: mdl-31556460

RESUMEN

Estrogen receptor alpha (ERα) activity is associated with increased cancer cell proliferation. Studies aiming to understand the impact of ERα on cancer-associated phenotypes have largely been limited to its transcriptional activity. Herein, we demonstrate that ERα coordinates its transcriptional output with selective modulation of mRNA translation. Importantly, translational perturbations caused by depletion of ERα largely manifest as "translational offsetting" of the transcriptome, whereby amounts of translated mRNAs and corresponding protein levels are maintained constant despite changes in mRNA abundance. Transcripts whose levels, but not polysome association, are reduced following ERα depletion lack features which limit translation efficiency including structured 5'UTRs and miRNA target sites. In contrast, mRNAs induced upon ERα depletion whose polysome association remains unaltered are enriched in codons requiring U34-modified tRNAs for efficient decoding. Consistently, ERα regulates levels of U34-modifying enzymes and thereby controls levels of U34-modified tRNAs. These findings unravel a hitherto unprecedented mechanism of ERα-dependent orchestration of transcriptional and translational programs that may be a pervasive mechanism of proteome maintenance in hormone-dependent cancers.


Asunto(s)
Neoplasias de la Mama/genética , Receptor alfa de Estrógeno/genética , Regulación Neoplásica de la Expresión Génica , Polirribosomas/genética , Biosíntesis de Proteínas , ARN Mensajero/genética , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Proliferación Celular , Receptor alfa de Estrógeno/metabolismo , Femenino , Humanos , Células MCF-7 , Polirribosomas/metabolismo , ARN Mensajero/metabolismo , Transducción de Señal , Activación Transcripcional
3.
PLoS Pathog ; 16(6): e1008291, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32479529

RESUMEN

The protozoan parasite Leishmania donovani (L. donovani) causes visceral leishmaniasis, a chronic infection which is fatal when untreated. Herein, we investigated whether in addition to altering transcription, L. donovani modulates host mRNA translation to establish a successful infection. Polysome-profiling revealed that one third of protein-coding mRNAs expressed in primary mouse macrophages are differentially translated upon infection with L. donovani promastigotes or amastigotes. Gene ontology analysis identified key biological processes enriched for translationally regulated mRNAs and were predicted to be either activated (e.g. chromatin remodeling and RNA metabolism) or inhibited (e.g. intracellular trafficking and antigen presentation) upon infection. Mechanistic in silico and biochemical analyses showed selective activation mTOR- and eIF4A-dependent mRNA translation, including transcripts encoding central regulators of mRNA turnover and inflammation (i.e. PABPC1, EIF2AK2, and TGF-ß). L. donovani survival within macrophages was favored under mTOR inhibition but was dampened by pharmacological blockade of eIF4A. Overall, this study uncovers a vast yet selective reprogramming of the host cell translational landscape early during L. donovani infection, and suggests that some of these changes are involved in host defense mechanisms while others are part of parasite-driven survival strategies. Further in vitro and in vivo investigation will shed light on the contribution of mTOR- and eIF4A-dependent translational programs to the outcome of visceral leishmaniasis.


Asunto(s)
Factor 4A Eucariótico de Iniciación/metabolismo , Leishmania donovani/metabolismo , Leishmaniasis Visceral , Macrófagos , Biosíntesis de Proteínas , ARN/metabolismo , Serina-Treonina Quinasas TOR/metabolismo , Animales , Leishmaniasis Visceral/metabolismo , Leishmaniasis Visceral/patología , Macrófagos/metabolismo , Macrófagos/parasitología , Macrófagos/patología , Ratones
4.
Nucleic Acids Res ; 47(12): e70, 2019 07 09.
Artículo en Inglés | MEDLINE | ID: mdl-30926999

RESUMEN

mRNA translation plays an evolutionarily conserved role in homeostasis and when dysregulated contributes to various disorders including metabolic and neurological diseases and cancer. Notwithstanding that optimal and universally applicable methods are critical for understanding the complex role of translational control under physiological and pathological conditions, approaches to analyze translatomes are largely underdeveloped. To address this, we developed the anota2seq algorithm which outperforms current methods for statistical identification of changes in translation. Notably, in contrast to available analytical methods, anota2seq also allows specific identification of an underappreciated mode of gene expression regulation whereby translation acts as a buffering mechanism which maintains protein levels despite fluctuations in corresponding mRNA abundance ('translational buffering'). Thus, the universal anota2seq algorithm allows efficient and hitherto unprecedented interrogation of translatomes which is anticipated to advance knowledge regarding the role of translation in homeostasis and disease.


Asunto(s)
Algoritmos , Biosíntesis de Proteínas , Interpretación Estadística de Datos , Análisis de Secuencia por Matrices de Oligonucleótidos , Proteínas/análisis , Proteínas Ribosómicas , Ribosomas , Análisis de Secuencia de ARN , Transcriptoma
5.
Biochim Biophys Acta Rev Cancer ; 1868(2): 484-499, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28947238

RESUMEN

Current anticancer paradigms largely target driver mutations considered integral for cancer cell survival and tumor progression. Although initially successful, many of these strategies are unable to overcome the tremendous heterogeneity that characterizes advanced tumors, resulting in the emergence of resistant disease. Cancer is a rapidly evolving, multifactorial disease that accumulates numerous genetic and epigenetic alterations. This results in wide phenotypic and molecular heterogeneity within the tumor, the complexity of which is further amplified through specific interactions between cancer cells and the tumor microenvironment. In this context, cancer may be perceived as an "ecomolecular" disease that involves cooperation between several neoplastic clones and their interactions with immune cells, stromal fibroblasts, and other cell types present in the microenvironment. This collaboration is mediated by a variety of secreted factors. Cancer is therefore analogous to complex ecosystems such as microbial consortia. In the present article, we comment on the current paradigms and perspectives guiding the development of cancer diagnostics and therapeutics and the potential application of systems biology to untangle the complexity of neoplasia. In our opinion, conceptualization of neoplasia as an ecomolecular disease is warranted. Advances in knowledge pertinent to the complexity and dynamics of interactions within the cancer ecosystem are likely to improve understanding of tumor etiology, pathogenesis, and progression. This knowledge is anticipated to facilitate the design of new and more effective therapeutic approaches that target the tumor ecosystem in its entirety.


Asunto(s)
Ecosistema , Neoplasias/etiología , Biología de Sistemas/métodos , Animales , Epigénesis Genética , Humanos , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Microambiente Tumoral
6.
J Immunol ; 200(12): 4102-4116, 2018 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-29712774

RESUMEN

Macrophages represent one of the first lines of defense during infections and are essential for resolution of inflammation following pathogen clearance. Rapid activation or suppression of protein synthesis via changes in translational efficiency allows cells of the immune system, including macrophages, to quickly respond to external triggers or cues without de novo mRNA synthesis. The translational repressors eIF4E-binding proteins 4E-BP1 and 4E-BP2 (4E-BP1/2) are central regulators of proinflammatory cytokine synthesis during viral and parasitic infections. However, it remains to be established whether 4E-BP1/2 play a role in translational control of anti-inflammatory responses. By comparing translational efficiencies of immune-related transcripts in macrophages from wild-type and 4E-BP1/2 double-knockout mice, we found that translation of mRNAs encoding two major regulators of inflammation, IL-10 and PG-endoperoxide synthase 2/cyclooxygenase-2, is controlled by 4E-BP1/2. Genetic deletion of 4E-BP1/2 in macrophages increased endogenous IL-10 and PGE2 protein synthesis in response to TLR4 stimulation and reduced their bactericidal capacity. The molecular mechanism involves enhanced anti-inflammatory gene expression (sIl1ra, Nfil3, Arg1, Serpinb2) owing to upregulation of IL-10-STAT3 and PGE2-C/EBPß signaling. These data provide evidence that 4E-BP1/2 limit anti-inflammatory responses in macrophages and suggest that dysregulated activity of 4E-BP1/2 might be involved in reprogramming of the translational and downstream transcriptional landscape of macrophages during pathological conditions, such as infections and cancer.


Asunto(s)
Proteínas Portadoras/metabolismo , Ciclooxigenasa 2/metabolismo , Factores Eucarióticos de Iniciación/metabolismo , Inflamación/metabolismo , Interleucina-10/metabolismo , Macrófagos/metabolismo , Fosfoproteínas/metabolismo , Proteínas Adaptadoras Transductoras de Señales , Animales , Proteínas de Ciclo Celular , Dinoprostona/metabolismo , Expresión Génica/fisiología , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Unión Proteica/fisiología , Biosíntesis de Proteínas/fisiología , ARN Mensajero/metabolismo , Proteínas Represoras/metabolismo , Transducción de Señal/fisiología , Transcripción Genética/fisiología , Regulación hacia Arriba/fisiología
7.
Nucleic Acids Res ; 46(1): e3, 2018 01 09.
Artículo en Inglés | MEDLINE | ID: mdl-29069469

RESUMEN

Polysome-profiling is commonly used to study translatomes and applies laborious extraction of efficiently translated mRNA (associated with >3 ribosomes) from a large volume across many fractions. This property makes polysome-profiling inconvenient for larger experimental designs or samples with low RNA amounts. To address this, we optimized a non-linear sucrose gradient which reproducibly enriches for efficiently translated mRNA in only one or two fractions, thereby reducing sample handling 5-10-fold. The technique generates polysome-associated RNA with a quality reflecting the starting material and, when coupled with smart-seq2 single-cell RNA sequencing, translatomes in small tissues from biobanks can be obtained. Translatomes acquired using optimized non-linear gradients resemble those obtained with the standard approach employing linear gradients. Polysome-profiling using optimized non-linear gradients in serum starved HCT-116 cells with or without p53 showed that p53 status associates with changes in mRNA abundance and translational efficiency leading to changes in protein levels. Moreover, p53 status also induced translational buffering whereby changes in mRNA levels are buffered at the level of mRNA translation. Thus, here we present a polysome-profiling technique applicable to large study designs, primary cells and frozen tissue samples such as those collected in biobanks.


Asunto(s)
Polirribosomas/metabolismo , Biosíntesis de Proteínas , ARN Mensajero/genética , Ribosomas/metabolismo , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Femenino , Células HCT116 , Humanos , Células MCF-7 , Mutación , ARN Mensajero/metabolismo , Análisis de Secuencia de ARN , Proteína p53 Supresora de Tumor/genética , Proteína p53 Supresora de Tumor/metabolismo
8.
Infect Immun ; 86(9)2018 09.
Artículo en Inglés | MEDLINE | ID: mdl-29967092

RESUMEN

The intracellular parasite Toxoplasma gondii promotes infection by targeting multiple host cell processes; however, whether it modulates mRNA translation is currently unknown. Here, we show that infection of primary murine macrophages with type I or II T. gondii strains causes a profound perturbation of the host cell translatome. Notably, translation of transcripts encoding proteins involved in metabolic activity and components of the translation machinery was activated upon infection. In contrast, the translational efficiency of mRNAs related to immune cell activation and cytoskeleton/cytoplasm organization was largely suppressed. Mechanistically, T. gondii bolstered mechanistic target of rapamycin (mTOR) signaling to selectively activate the translation of mTOR-sensitive mRNAs, including those with a 5'-terminal oligopyrimidine (5' TOP) motif and those encoding mitochondrion-related proteins. Consistent with parasite modulation of host mTOR-sensitive translation to promote infection, inhibition of mTOR activity suppressed T. gondii replication. Thus, selective reprogramming of host mRNA translation represents an important subversion strategy during T. gondii infection.


Asunto(s)
Interacciones Huésped-Parásitos , Macrófagos/parasitología , Biosíntesis de Proteínas/genética , Toxoplasma/patogenicidad , Animales , Células Cultivadas , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Proteínas Mitocondriales/genética , Proteínas Protozoarias/inmunología , Secuencia de Oligopirimidina en la Región 5' Terminal del ARN , Transducción de Señal , Serina-Treonina Quinasas TOR/genética
9.
Br J Cancer ; 118(4): 480-488, 2018 02 20.
Artículo en Inglés | MEDLINE | ID: mdl-29370583

RESUMEN

BACKGROUND: Transcriptomic profiles have shown promise as predictors of response to neoadjuvant chemotherapy in breast cancer (BC). This study aimed to explore their predictive value in the advanced BC (ABC) setting. METHODS: In a Phase 3 trial of first-line chemotherapy in ABC, a fine needle aspiration biopsy (FNAB) was obtained at baseline. Intrinsic molecular subtypes and gene modules related to immune response, proliferation, oestrogen receptor (ER) signalling and recurring genetic alterations were analysed for association with objective response to chemotherapy. Gene-set enrichment analysis (GSEA) of responders vs non-responders was performed independently. Lymphocytes were enumerated in FNAB smears and the absolute abundance of immune cell types was calculated using the Microenvironment Cell Populations counter method. RESULTS: Gene expression data were available for 109 patients. Objective response to chemotherapy was statistically significantly associated with an immune module score (odds ratio (OR)=1.62; 95% confidence interval (CI), 1.03-2.64; P=0.04). Subgroup analysis showed that this association was restricted to patients with ER-positive or luminal tumours (OR=3.54; 95%, 1.43-10.86; P=0.012 and P for interaction=0.04). Gene-set enrichment analysis confirmed that in these subgroups, immune-related gene sets were enriched in responders. CONCLUSIONS: Immune-related transcriptional signatures may predict response to chemotherapy in ER-positive and luminal ABC.


Asunto(s)
Neoplasias de la Mama/tratamiento farmacológico , Capecitabina/administración & dosificación , Epirrubicina/administración & dosificación , Redes Reguladoras de Genes/efectos de los fármacos , Paclitaxel/administración & dosificación , Protocolos de Quimioterapia Combinada Antineoplásica/administración & dosificación , Protocolos de Quimioterapia Combinada Antineoplásica/farmacología , Biopsia con Aguja Fina , Neoplasias de la Mama/genética , Neoplasias de la Mama/inmunología , Neoplasias de la Mama/patología , Capecitabina/farmacología , Epirrubicina/farmacología , Femenino , Perfilación de la Expresión Génica/métodos , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Humanos , Persona de Mediana Edad , Paclitaxel/farmacología , Análisis de Supervivencia , Resultado del Tratamiento
10.
Blood ; 128(11): 1475-89, 2016 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-27465917

RESUMEN

Treatment of hematological malignancies by adoptive transfer of activated natural killer (NK) cells is limited by poor postinfusion persistence. We compared the ability of interleukin-2 (IL-2) and IL-15 to sustain human NK-cell functions following cytokine withdrawal to model postinfusion performance. In contrast to IL-2, IL-15 mediated stronger signaling through the IL-2/15 receptor complex and provided cell function advantages. Genome-wide analysis of cytosolic and polysome-associated messenger RNA (mRNA) revealed not only cytokine-dependent differential mRNA levels and translation during cytokine activation but also that most gene expression differences were primed by IL-15 and only manifested after cytokine withdrawal. IL-15 augmented mammalian target of rapamycin (mTOR) signaling, which correlated with increased expression of genes related to cell metabolism and respiration. Consistently, mTOR inhibition abrogated IL-15-induced cell function advantages. Moreover, mTOR-independent STAT-5 signaling contributed to improved NK-cell function during cytokine activation but not following cytokine withdrawal. The superior performance of IL-15-stimulated NK cells was also observed using a clinically applicable protocol for NK-cell expansion in vitro and in vivo. Finally, expression of IL-15 correlated with cytolytic immune functions in patients with B-cell lymphoma and favorable clinical outcome. These findings highlight the importance of mTOR-regulated metabolic processes for immune cell functions and argue for implementation of IL-15 in adoptive NK-cell cancer therapy.


Asunto(s)
Citotoxicidad Inmunológica/inmunología , Inmunoterapia Adoptiva , Interleucina-15/farmacología , Células Asesinas Naturales/inmunología , Neoplasias Experimentales/terapia , Serina-Treonina Quinasas TOR/metabolismo , Animales , Proteínas de Ciclo Celular/genética , Citocinas/metabolismo , Humanos , Células Asesinas Naturales/metabolismo , Células Asesinas Naturales/patología , Activación de Linfocitos , Ratones Endogámicos NOD , Ratones SCID , Proteínas Mitocondriales/genética , Neoplasias Experimentales/inmunología , Neoplasias Experimentales/patología , Transducción de Señal
11.
Breast Cancer Res Treat ; 147(2): 407-14, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25129344

RESUMEN

The purpose of this study is to determine the prognostic role of Ki67 evaluated in relapse biopsies from patients with metastatic breast cancer (MBC). Two hundred and ten patients diagnosed with MBC in Stockholm, Sweden between 1998 and 2009 and with Ki67 assessed at time of first systemic relapse (mKi67) were retrospectively identified and divided into two groups according to mKi67 fraction (low ≤20 %, high >20 %). Post-relapse survival was compared between the groups using Kaplan-Meier and Cox regression methods. Death rate as function of continuous mKi67 was also evaluated. Furthermore, the prognostic role of intra-individual change in Ki67 between primary tumor and matched metastasis was explored by Kaplan-Meier plots. One hundred and twenty-five patients had low and 85 had high mKi67. Median survival was 25 and 17 months in low- and high-mKi67 group, respectively [hazard ratio (HR) 0.69, 95 % confidence intervals (CI) 0.51-0.92, P = 0.01]. In a multivariate model adjusted for prognostic confounders, low-mKi67 showed a non-significant trend toward better survival (HR 0.85, 95 %CI 0.62-1.16, P = 0.30). Nevertheless, mKi67 independently correlated with survival when compared with primary tumor proliferation (HR 0.56, 95 %CI 0.38-0.81, P = 0.002). The 2-year death rate steeply increased as mKi67 increased. Moreover, the change from high in primary tumor to low in metastasis significantly correlated with longer survival when compared with stable Ki67 levels (HR 0.48, 95 %CI 0.31-0.76, P = 0.002). In this cohort of MBC patients, mKi67 inversely but not independently correlated with survival. However, a significant association between mKi67 and survival was shown regardless of primary tumor proliferation.


Asunto(s)
Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/patología , Antígeno Ki-67/metabolismo , Femenino , Humanos , Estimación de Kaplan-Meier , Persona de Mediana Edad , Metástasis de la Neoplasia , Recurrencia Local de Neoplasia/metabolismo , Recurrencia Local de Neoplasia/patología , Pronóstico , Estudios Retrospectivos , Suecia
12.
EMBO Mol Med ; 16(9): 1986-2001, 2024 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-39060641

RESUMEN

Darier disease (DD) is a rare severe acantholytic skin disease caused by mutations in the ATP2A2 gene that encodes for the sarco/endoplasmic reticulum calcium ATPase isoform 2 (SERCA2). SERCA2 maintains endoplasmic reticulum calcium homeostasis by pumping calcium into the ER, critical for regulating cellular calcium dynamics and cellular function. To date, there is no treatment that specifically targets the disease mechanisms in DD. Dantrolene sodium (Dl) is a ryanodine receptor antagonist that inhibits calcium release from ER to increase ER calcium levels and is currently used for non-dermatological indications. In this study, we first identified dysregulated genes and molecular pathways in DD patient skin, demonstrating downregulation of cell adhesion and calcium homeostasis pathways, as well as upregulation of ER stress and apoptosis. We then show in various in vitro models of DD and SERCA2 inhibition that Dl aided in the retention of ER calcium and promoted cell adhesion. In addition, Dl treatment reduced ER stress and suppressed apoptosis. Our findings suggest that Dl specifically targets pathogenic mechanisms of DD and may be a potential treatment.


Asunto(s)
Calcio , Dantroleno , Enfermedad de Darier , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico , Dantroleno/farmacología , Dantroleno/uso terapéutico , Enfermedad de Darier/tratamiento farmacológico , Enfermedad de Darier/metabolismo , Humanos , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico/metabolismo , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico/genética , Calcio/metabolismo , Apoptosis/efectos de los fármacos , Adhesión Celular/efectos de los fármacos , Estrés del Retículo Endoplásmico/efectos de los fármacos , Retículo Endoplásmico/metabolismo , Retículo Endoplásmico/efectos de los fármacos , Piel/patología , Piel/efectos de los fármacos , Piel/metabolismo
13.
Front Immunol ; 14: 1151754, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-37063885

RESUMEN

Mast cells are tissue-resident cells playing major roles in homeostasis and disease conditions. Lung mast cells are particularly important in airway inflammatory diseases such as asthma. Human mast cells are classically divided into the subsets MCT and MCTC, where MCT express the mast cell protease tryptase and MCTC in addition express chymase, carboxypeptidase A3 (CPA3) and cathepsin G. Apart from the disctintion of the MCT and MCTC subsets, little is known about the heterogeniety of human lung mast cells and a deep analysis of their heterogeniety has previously not been performed. We therefore performed single cell RNA sequencing on sorted human lung mast cells using SmartSeq2. The mast cells showed high expression of classical mast cell markers. The expression of several individual genes varied considerably among the cells, however, no subpopulations were detected by unbiased clustering. Variable genes included the protease-encoding transcripts CMA1 (chymase) and CTSG (cathepsin G). Human lung mast cells are predominantly of the MCT subset and consistent with this, the expression of CMA1 was only detectable in a small proportion of the cells, and correlated moderately to CTSG. However, in contrast to established data for the protein, CPA3 mRNA was high in all cells and the correlation of CPA3 to CMA1 was weak.


Asunto(s)
Mastocitos , Péptido Hidrolasas , Humanos , Quimasas/genética , Quimasas/metabolismo , Mastocitos/metabolismo , Catepsina G , Péptido Hidrolasas/metabolismo , Triptasas/genética , Triptasas/metabolismo , Pulmón/metabolismo , Análisis de Secuencia de ARN
14.
Stat Appl Genet Mol Biol ; 10: Article 14, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21381439

RESUMEN

The integration of multiple high-dimensional data sets (omics data) has been a very active but challenging area of bioinformatics research in recent years. Various adaptations of non-standard multivariate statistical tools have been suggested that allow to analyze and visualize such data sets simultaneously. However, these methods typically can deal with two data sets only, whereas systems biology experiments often generate larger numbers of high-dimensional data sets. For this reason, we suggest an explorative analysis of similarity between data sets as an initial analysis steps. This analysis is based on the RV coefficient, a matrix correlation, that can be interpreted as a generalization of the squared correlation from two single variables to two sets of variables. It has been shown before however that the high-dimensionality of the data introduces substantial bias to the RV. We therefore introduce an alternative version, the adjusted RV, which is unbiased in the case of independent data sets. We can also show that in many situations, particularly for very high-dimensional data sets, the adjusted RV is a better estimator than previously RV versions in terms of the mean square error and the power of the independence test based on it. We demonstrate the usefulness of the adjusted RV by applying it to data set of 19 different multivariate data sets from a systems biology experiment. The pairwise RV values between the data sets define a similarity matrix that we can use as an input to a hierarchical clustering or a multidimensional scaling. We show that this reveals biological meaningful subgroups of data sets in our study.


Asunto(s)
Minería de Datos/métodos , Bases de Datos Factuales/estadística & datos numéricos , Biometría/métodos , Análisis por Conglomerados , Biología Computacional/métodos , Simulación por Computador , Humanos , Análisis Multivariante
15.
Nat Commun ; 13(1): 1100, 2022 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-35232962

RESUMEN

Despite the success of therapies targeting oncogenes in cancer, clinical outcomes are limited by residual disease that ultimately results in relapse. This residual disease is often characterized by non-genetic adaptive resistance, that in melanoma is characterised by altered metabolism. Here, we examine how targeted therapy reprograms metabolism in BRAF-mutant melanoma cells using a genome-wide RNA interference (RNAi) screen and global gene expression profiling. Using this systematic approach we demonstrate post-transcriptional regulation of metabolism following BRAF inhibition, involving selective mRNA transport and translation. As proof of concept we demonstrate the RNA processing kinase U2AF homology motif kinase 1 (UHMK1) associates with mRNAs encoding metabolism proteins and selectively controls their transport and translation during adaptation to BRAF-targeted therapy. UHMK1 inactivation induces cell death by disrupting therapy induced metabolic reprogramming, and importantly, delays resistance to BRAF and MEK combination therapy in multiple in vivo models. We propose selective mRNA processing and translation by UHMK1 constitutes a mechanism of non-genetic resistance to targeted therapy in melanoma by controlling metabolic plasticity induced by therapy.


Asunto(s)
Melanoma , Proteínas Proto-Oncogénicas B-raf , Humanos , Melanoma/tratamiento farmacológico , Melanoma/genética , Melanoma/metabolismo , Terapia Molecular Dirigida , Mutación , Recurrencia Local de Neoplasia/tratamiento farmacológico , Inhibidores de Proteínas Quinasas/farmacología , Proteínas Proto-Oncogénicas B-raf/metabolismo , ARN Mensajero/uso terapéutico
16.
Nat Commun ; 10(1): 3589, 2019 08 09.
Artículo en Inglés | MEDLINE | ID: mdl-31399573

RESUMEN

Overcoming cellular growth restriction, including the evasion of cellular senescence, is a hallmark of cancer. We report that PAK4 is overexpressed in all human breast cancer subtypes and associated with poor patient outcome. In mice, MMTV-PAK4 overexpression promotes spontaneous mammary cancer, while PAK4 gene depletion delays MMTV-PyMT driven tumors. Importantly, PAK4 prevents senescence-like growth arrest in breast cancer cells in vitro, in vivo and ex vivo, but is not needed in non-immortalized cells, while PAK4 overexpression in untransformed human mammary epithelial cells abrogates H-RAS-V12-induced senescence. Mechanistically, a PAK4 - RELB - C/EBPß axis controls the senescence-like growth arrest and a PAK4 phosphorylation residue (RELB-Ser151) is critical for RELB-DNA interaction, transcriptional activity and expression of the senescence regulator C/EBPß. These findings establish PAK4 as a promoter of breast cancer that can overcome oncogene-induced senescence and reveal a selective vulnerability of cancer to PAK4 inhibition.


Asunto(s)
Neoplasias de la Mama/patología , Factor de Transcripción ReIB/metabolismo , Quinasas p21 Activadas/metabolismo , Animales , Mama/citología , Mama/patología , Neoplasias de la Mama/mortalidad , Línea Celular Tumoral , Senescencia Celular/genética , Células Epiteliales , Femenino , Técnicas de Silenciamiento del Gen , Humanos , Glándulas Mamarias Animales/patología , Neoplasias Mamarias Experimentales/genética , Neoplasias Mamarias Experimentales/patología , Ratones , Ratones Transgénicos , Persona de Mediana Edad , Cultivo Primario de Células , Pronóstico , Ensayos Antitumor por Modelo de Xenoinjerto , Quinasas p21 Activadas/genética
17.
Mol Oncol ; 10(4): 517-25, 2016 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-26651914

RESUMEN

Molecular subtypes and gene expression signatures are widely used in early breast cancer but their role in metastatic disease is less explored. Two hundred-twenty patients diagnosed with primary breast cancer and subsequent relapse in Stockholm, Sweden between 1997 and 2006 were identified and their primary tumor was assessed for immunohistochemistry (IHC)- and PAM50-based subtypes, risk of recurrence (ROR-S) score, 21-gene and 70-gene signatures using research-based microarray expression profiles. Clinical and pathological data were retrospectively collected. Post-relapse survival within intrinsic subtypes and genomic signatures was investigated by Kaplan-Meier and Cox regression methods. ROR weighted for proliferation index (ROR-P) was explored and the prognostic contribution provided when combined to a clinical model estimated as change in LR- χ(2). IHC classified 27%, 24%, 36% and 13% of the tumors as luminal A, luminal B, HER2+ and triple negative, respectively. PAM50 categorized 22%, 24%, 26%, 22%, 6% of the tumors as luminal A, luminal B, HER2-enriched, basal-like and normal-like. Triple negative and basal tumors had a significantly shorter median post-relapse survival in comparison with luminal. Overall, neither IHC nor PAM50 subtypes, 21- and 70- gene profiles were prognostic in multivariable models. Low and medium ROR-S had a longer survival compared with the high-risk group (23 vs 10 months; p = 0.04). ROR-P independently correlated with post-relapse survival (p = 0.002) and provided the most significant prognostic information when added to a clinical model. ROR score from primary tumor represents an independent prognostic factor of post-relapse survival beyond classical clinical and pathological variables.


Asunto(s)
Neoplasias de la Mama , Proliferación Celular , Regulación Neoplásica de la Expresión Génica , Proteínas de Neoplasias/biosíntesis , Recurrencia Local de Neoplasia , Anciano , Neoplasias de la Mama/metabolismo , Neoplasias de la Mama/mortalidad , Neoplasias de la Mama/patología , Neoplasias de la Mama/terapia , Supervivencia sin Enfermedad , Femenino , Humanos , Persona de Mediana Edad , Recurrencia Local de Neoplasia/metabolismo , Recurrencia Local de Neoplasia/mortalidad , Recurrencia Local de Neoplasia/patología , Recurrencia Local de Neoplasia/terapia , Estudios Retrospectivos , Tasa de Supervivencia
18.
Oncotarget ; 6(41): 43853-68, 2015 Dec 22.
Artículo en Inglés | MEDLINE | ID: mdl-26554417

RESUMEN

Estrogen receptor alpha (ERα) is highly expressed in most breast cancers. Consequently, ERα modulators, such as tamoxifen, are successful in breast cancer treatment, although tamoxifen resistance is commonly observed. While tamoxifen resistance may be caused by altered ERα signaling, the molecular mechanisms regulating ERα signaling and tamoxifen resistance are not entirely clear. Here, we found that PAK4 expression was consistently correlated to poor patient outcome in endocrine treated and tamoxifen-only treated breast cancer patients. Importantly, while PAK4 overexpression promoted tamoxifen resistance in MCF-7 human breast cancer cells, pharmacological treatment with a group II PAK (PAK4, 5, 6) inhibitor, GNE-2861, sensitized tamoxifen resistant MCF-7/LCC2 breast cancer cells to tamoxifen. Mechanistically, we identified a regulatory positive feedback loop, where ERα bound to the PAK4 gene, thereby promoting PAK4 expression, while PAK4 in turn stabilized the ERα protein, activated ERα transcriptional activity and ERα target gene expression. Further, PAK4 phosphorylated ERα-Ser305, a phosphorylation event needed for the PAK4 activation of ERα-dependent transcription. In conclusion, PAK4 may be a suitable target for perturbing ERα signaling and tamoxifen resistance in breast cancer patients.


Asunto(s)
Bencimidazoles/farmacología , Neoplasias de la Mama/metabolismo , Resistencia a Antineoplásicos/efectos de los fármacos , Inhibidores Enzimáticos/farmacología , Receptor alfa de Estrógeno/metabolismo , Pirimidinas/farmacología , Quinasas p21 Activadas/metabolismo , Neoplasias de la Mama/mortalidad , Neoplasias de la Mama/patología , Bases de Datos Genéticas , Resistencia a Antineoplásicos/fisiología , Femenino , Citometría de Flujo , Humanos , Immunoblotting , Estimación de Kaplan-Meier , Células MCF-7 , Reacción en Cadena de la Polimerasa , ARN Interferente Pequeño , Moduladores Selectivos de los Receptores de Estrógeno/farmacología , Transducción de Señal/fisiología , Tamoxifeno/farmacología , Transfección
19.
J Clin Oncol ; 30(2): 191-9, 2012 Jan 10.
Artículo en Inglés | MEDLINE | ID: mdl-22162575

RESUMEN

PURPOSE: This is the first randomized phase II/III trial comparing two carboplatin-based chemotherapy regimens in patients with urothelial cancer who are ineligible ("unfit") for cisplatin chemotherapy. PATIENTS AND METHODS: The primary objective of the phase III part of this study was to compare the overall survival (OS) of chemotherapy-naive patients with measurable disease and an impaired renal function (glomerular filtration rate < 60 but > 30 mL/min) and/or performance score of 2 who were randomly assigned to receive either gemcitabine/carboplatin (GC) or methotrexate/carboplatin/vinblastine (M-CAVI). To detect an increase of 50% in median survival with GC compared with M-CAVI (13.5 v 9 months) based on a two-sided log-rank test at error rates α = .05 and ß = .20, 225 patients were required. Secondary end points were overall response rate (ORR), progression-free survival (PFS), toxicity, and quality of life. RESULTS: In all, 238 patients were randomly assigned by 29 institutions over a period of 7 years. The median follow-up was 4.5 years. Best ORRs were 41.2% (36.1% confirmed response) for patients receiving GC versus 30.3% (21.0% confirmed response) for patients receiving M-CAVI (P = .08). Median OS was 9.3 months in the GC arm and 8.1 months in the M-CAVI arm (P = .64). There was no difference in PFS (P = .78) between the two arms. Severe acute toxicity (death, grade 4 thrombocytopenia with bleeding, grade 3 or 4 renal toxicity, neutropenic fever, or mucositis) was observed in 9.3% of patients receiving GC and 21.2% of patients receiving M-CAVI. CONCLUSION: There were no significant differences in efficacy between the two treatment groups. The incidence of severe acute toxicities was higher for those receiving M-CAVI.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Neoplasias Urológicas/tratamiento farmacológico , Adulto , Anciano , Anciano de 80 o más Años , Carboplatino/administración & dosificación , Cisplatino , Contraindicaciones , Desoxicitidina/administración & dosificación , Desoxicitidina/análogos & derivados , Femenino , Humanos , Masculino , Metotrexato/administración & dosificación , Persona de Mediana Edad , Calidad de Vida , Encuestas y Cuestionarios , Tasa de Supervivencia , Vinblastina/administración & dosificación , Gemcitabina
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