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1.
Breast Cancer Res ; 26(1): 54, 2024 Mar 29.
Artículo en Inglés | MEDLINE | ID: mdl-38553760

RESUMEN

Fibroblast growth factors (FGFs) control various cellular functions through fibroblast growth factor receptor (FGFR) activation, including proliferation, differentiation, migration, and survival. FGFR amplification in ER + breast cancer patients correlate with poor prognosis, and FGFR inhibitors are currently being tested in clinical trials. By comparing three-dimensional spheroid growth of ER + breast cancer cells with and without FGFR1 amplification, our research discovered that FGF2 treatment can paradoxically decrease proliferation in cells with FGFR1 amplification or overexpression. In contrast, FGF2 treatment in cells without FGFR1 amplification promotes classical FGFR proliferative signaling through the MAPK cascade. The growth inhibitory effect of FGF2 in FGFR1 amplified cells aligned with an increase in p21, a cell cycle inhibitor that hinders the G1 to S phase transition in the cell cycle. Additionally, FGF2 addition in FGFR1 amplified cells activated JAK-STAT signaling and promoted a stem cell-like state. FGF2-induced paradoxical effects were reversed by inhibiting p21 or the JAK-STAT pathway and with pan-FGFR inhibitors. Analysis of patient ER + breast tumor transcriptomes from the TCGA and METABRIC datasets demonstrated a strong positive association between expression of FGF2 and stemness signatures, which was further enhanced in tumors with high FGFR1 expression. Overall, our findings reveal a divergence in FGFR signaling, transitioning from a proliferative to stemness state driven by activation of JAK-STAT signaling and modulation of p21 levels. Activation of these divergent signaling pathways in FGFR amplified cancer cells and paradoxical growth effects highlight a challenge in the use of FGFR inhibitors in cancer treatment.


Asunto(s)
Neoplasias de la Mama , Transducción de Señal , Humanos , Femenino , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Factor 2 de Crecimiento de Fibroblastos/metabolismo , Factor 2 de Crecimiento de Fibroblastos/farmacología , Factor 2 de Crecimiento de Fibroblastos/uso terapéutico , Quinasas Janus/metabolismo , Quinasas Janus/farmacología , Quinasas Janus/uso terapéutico , Factores de Transcripción STAT/metabolismo , Factores de Transcripción STAT/farmacología , Factores de Transcripción STAT/uso terapéutico , Receptor Tipo 1 de Factor de Crecimiento de Fibroblastos , Proliferación Celular , Factores de Crecimiento de Fibroblastos/farmacología , Línea Celular Tumoral
2.
Brief Bioinform ; 22(5)2021 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-33681983

RESUMEN

Single-cell RNA sequencing (scRNA-Seq) is an emerging strategy for characterizing immune cell populations. Compared to flow or mass cytometry, scRNA-Seq could potentially identify cell types and activation states that lack precise cell surface markers. However, scRNA-Seq is currently limited due to the need to manually classify each immune cell from its transcriptional profile. While recently developed algorithms accurately annotate coarse cell types (e.g. T cells versus macrophages), making fine distinctions (e.g. CD8+ effector memory T cells) remains a difficult challenge. To address this, we developed a machine learning classifier called ImmClassifier that leverages a hierarchical ontology of cell type. We demonstrate that its predictions are highly concordant with flow-based markers from CITE-seq and outperforms other tools (+15% recall, +14% precision) in distinguishing fine-grained cell types with comparable performance on coarse ones. Thus, ImmClassifier can be used to explore more deeply the heterogeneity of the immune system in scRNA-Seq experiments.


Asunto(s)
Aprendizaje Profundo , Células Eritroides/clasificación , Linfocitos/clasificación , ARN/genética , Análisis de la Célula Individual/métodos , Análisis por Conglomerados , Conjuntos de Datos como Asunto , Células Eritroides/citología , Células Eritroides/inmunología , Humanos , Inmunofenotipificación , Linfocitos/citología , Linfocitos/inmunología , ARN/inmunología , RNA-Seq , Análisis de Secuencia de ARN
3.
Mol Syst Biol ; 18(6): e10558, 2022 06.
Artículo en Inglés | MEDLINE | ID: mdl-35671075

RESUMEN

Advanced and metastatic estrogen receptor-positive (ER+ ) breast cancers are often endocrine resistant. However, endocrine therapy remains the primary treatment for all advanced ER+ breast cancers. Treatment options that may benefit resistant cancers, such as add-on drugs that target resistance pathways or switching to chemotherapy, are only available after progression on endocrine therapy. Here we developed an endocrine therapy prognostic model for early and advanced ER+ breast cancers. The endocrine resistance (ENDORSE) model is composed of two components, each based on the empirical cumulative distribution function of ranked expression of gene signatures. These signatures include a feature set associated with long-term survival outcomes on endocrine therapy selected using lasso-regularized Cox regression and a pathway-based curated set of genes expressed in response to estrogen. We extensively validated ENDORSE in multiple ER+ clinical trial datasets and demonstrated superior and consistent performance of the model over clinical covariates, proliferation markers, and multiple published signatures. Finally, genomic and pathway analyses in patient data revealed possible mechanisms that may help develop rational stratification strategies for endocrine-resistant ER+ breast cancer patients.


Asunto(s)
Neoplasias de la Mama , Neoplasias de la Mama/tratamiento farmacológico , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Resistencia a Antineoplásicos/genética , Estrógenos , Femenino , Humanos , Pronóstico , Receptores de Estrógenos/genética , Receptores de Estrógenos/metabolismo , Receptores de Estrógenos/uso terapéutico
4.
Proc Natl Acad Sci U S A ; 117(27): 16072-16082, 2020 07 07.
Artículo en Inglés | MEDLINE | ID: mdl-32571915

RESUMEN

The extent to which immune cell phenotypes in the peripheral blood reflect within-tumor immune activity prior to and early in cancer therapy is unclear. To address this question, we studied the population dynamics of tumor and immune cells, and immune phenotypic changes, using clinical tumor and immune cell measurements and single-cell genomic analyses. These samples were serially obtained from a cohort of advanced gastrointestinal cancer patients enrolled in a trial with chemotherapy and immunotherapy. Using an ecological population model, fitted to clinical tumor burden and immune cell abundance data from each patient, we find evidence of a strong tumor-circulating immune cell interaction in responder patients but not in those patients that progress on treatment. Upon initiation of therapy, immune cell abundance increased rapidly in responsive patients, and once the peak level is reached tumor burden decreases, similar to models of predator-prey interactions; these dynamic patterns were absent in nonresponder patients. To interrogate phenotype dynamics of circulating immune cells, we performed single-cell RNA sequencing at serial time points during treatment. These data show that peripheral immune cell phenotypes were linked to the increased strength of patients' tumor-immune cell interaction, including increased cytotoxic differentiation and strong activation of interferon signaling in peripheral T cells in responder patients. Joint modeling of clinical and genomic data highlights the interactions between tumor and immune cell populations and reveals how variation in patient responsiveness can be explained by differences in peripheral immune cell signaling and differentiation soon after the initiation of immunotherapy.


Asunto(s)
Comunicación Celular/inmunología , Inmunoterapia/métodos , Neoplasias/inmunología , Neoplasias/terapia , Fenotipo , Microambiente Tumoral/inmunología , Regulación de la Expresión Génica , Humanos , Factores Inmunológicos/genética , Factores Inmunológicos/inmunología , Monocitos/inmunología , Análisis de Secuencia de ARN , Análisis de la Célula Individual , Linfocitos T/inmunología
5.
Mar Drugs ; 19(1)2021 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-33477536

RESUMEN

Patients diagnosed with basal-like breast cancer suffer from poor prognosis and limited treatment options. There is an urgent need to identify new targets that can benefit patients with basal-like and claudin-low (BL-CL) breast cancers. We screened fractions from our Marine Invertebrate Compound Library (MICL) to identify compounds that specifically target BL-CL breast cancers. We identified a previously unreported trisulfated sterol, i.e., topsentinol L trisulfate (TLT), which exhibited increased efficacy against BL-CL breast cancers relative to luminal/HER2+ breast cancer. Biochemical investigation of the effects of TLT on BL-CL cell lines revealed its ability to inhibit activation of AMP-activated protein kinase (AMPK) and checkpoint kinase 1 (CHK1) and to promote activation of p38. The importance of targeting AMPK and CHK1 in BL-CL cell lines was validated by treating a panel of breast cancer cell lines with known small molecule inhibitors of AMPK (dorsomorphin) and CHK1 (Ly2603618) and recording the increased effectiveness against BL-CL breast cancers as compared with luminal/HER2+ breast cancer. Finally, we generated a drug response gene-expression signature and projected it against a human tumor panel of 12 different cancer types to identify other cancer types sensitive to the compound. The TLT sensitivity gene-expression signature identified breast and bladder cancer as the most sensitive to TLT, while glioblastoma multiforme was the least sensitive.


Asunto(s)
Antineoplásicos/farmacología , Neoplasias de la Mama/tratamiento farmacológico , Esteroles/farmacología , Proteínas Quinasas Activadas por AMP/efectos de los fármacos , Proteínas Quinasas Activadas por AMP/metabolismo , Antineoplásicos/química , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Línea Celular Tumoral , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/efectos de los fármacos , Quinasa 1 Reguladora del Ciclo Celular (Checkpoint 1)/metabolismo , Claudinas/metabolismo , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Esteroles/química , Proteínas Quinasas p38 Activadas por Mitógenos/efectos de los fármacos , Proteínas Quinasas p38 Activadas por Mitógenos/metabolismo
6.
Cancer Cell Int ; 20: 253, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32565737

RESUMEN

BACKGROUND: CDK4/6 inhibitors such as ribociclib are becoming widely used targeted therapies in hormone-receptor-positive (HR+) human epidermal growth factor receptor 2-negative (HER2-) breast cancer. However, cancers can advance due to drug resistance, a problem in which tumor heterogeneity and evolution are key features. METHODS: Ribociclib-resistant HR+/HER2- CAMA-1 breast cancer cells were generated through long-term ribociclib treatment. Characterization of sensitive and resistant cells were performed using RNA sequencing and whole exome sequencing. Lentiviral labeling with different fluorescent proteins enabled us to track the proliferation of sensitive and resistant cells under different treatments in a heterogeneous, 3D spheroid coculture system using imaging microscopy and flow cytometry. RESULTS: Transcriptional profiling of sensitive and resistant cells revealed the downregulation of the G2/M checkpoint in the resistant cells. Exploiting this acquired vulnerability; resistant cells exhibited collateral sensitivity for the Wee-1 inhibitor, adavosertib (AZD1775). The combination of ribociclib and adavosertib achieved additional antiproliferative effect exclusively in the cocultures compared to monocultures, while decreasing the selection for resistant cells. CONCLUSIONS: Our results suggest that optimal antiproliferative effects in heterogeneous cancers can be achieved via an integrative therapeutic approach targeting sensitive and resistant cancer cell populations within a tumor, respectively.

7.
BMC Cancer ; 19(1): 881, 2019 Sep 05.
Artículo en Inglés | MEDLINE | ID: mdl-31488082

RESUMEN

BACKGROUND: Gene expression profiling of rare cancers has proven challenging due to limited access to patient materials and requirement of intact, non-degraded RNA for next-generation sequencing. We customized a gene expression panel compatible with degraded RNA from formalin-fixed, paraffin-embedded (FFPE) patient cancer samples and investigated its utility in pathway activity profiling in patients with metaplastic breast cancer (MpBC). METHODS: Activity of various biological pathways was profiled in samples from nineteen patients with MpBC and 8 patients with invasive ductal carcinoma with triple negative breast cancer (TNBC) phenotype using a custom gene expression-based assay of 345 genes. RESULTS: MpBC samples of mesenchymal (chondroid and/or osteoid) histology demonstrated increased SNAI1 and BCL2L11 pathway activity compared to samples with non-mesenchymal histology. Additionally, late cornified envelope and keratinization genes were downregulated in MpBC compared to TNBC, and epithelial-to-mesenchymal transition (EMT) and collagen genes were upregulated in MpBC. Patients with high activity of an invasiveness gene expression signature, as well as high expression of the mesenchymal marker and extracellular matrix glycoprotein gene SPARC, experienced worse outcomes than those with low invasiveness activity and low SPARC expression. CONCLUSIONS: This study demonstrates the utility of gene expression profiling of metaplastic breast cancer FFPE samples with a custom counts-based assay. Gene expression patterns identified by this assay suggest that, although often histologically triple negative, patients with MpBC have distinct pathway activation compared to patients with invasive ductal TNBC. Incorporation of targeted therapies may lead to improved outcome for MpBC patients, especially in those patients expressing increased activity of invasiveness pathways.


Asunto(s)
Carcinoma Ductal de Mama/genética , Receptores de Factores de Crecimiento/metabolismo , Transducción de Señal/genética , Transcriptoma/genética , Neoplasias de la Mama Triple Negativas/genética , Adulto , Anciano , Anciano de 80 o más Años , Proteína 11 Similar a Bcl2/metabolismo , Carcinoma Ductal de Mama/patología , Estudios de Cohortes , Transición Epitelial-Mesenquimal/genética , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Persona de Mediana Edad , Osteonectina/genética , Fenotipo , Pronóstico , RNA-Seq/métodos , Factores de Transcripción de la Familia Snail/metabolismo , Neoplasias de la Mama Triple Negativas/patología
8.
Semin Cell Dev Biol ; 58: 108-17, 2016 10.
Artículo en Inglés | MEDLINE | ID: mdl-27338857

RESUMEN

The rise in genomic knowledge over the past decade has revealed the molecular etiology of many diseases, and has identified intricate signaling network activity in human cancers. Genomics provides the opportunity to determine genome structure and capture the activity of thousands of molecular events concurrently, which is important for deciphering highly complex genetic diseases such as cancer. In this review, we focus on genomic efforts directed towards one of cancer's most frequently mutated networks, the RAS pathway. Genomic tools such as gene expression signatures and assessment of mutations across the RAS network enable the capture of RAS signaling complexity. Due to this high level of interaction and cross-talk within the network, efforts to target RAS signaling in the clinic have generally failed, and we currently lack the ability to directly inhibit the RAS protein with high efficacy. We propose that the use of gene expression data can identify effective treatments that broadly inhibit the RAS network as this approach measures pathway activity independent of mutation status or any single mechanism of activation. Here, we review the genomic studies that map the complexity of the RAS network in cancer, and that show how genomic measurements of RAS pathway activation can identify effective RAS inhibition strategies. We also address the challenges and future directions for treating RAS-driven tumors. In summary, genomic assessment of RAS signaling provides a level of complexity necessary to accurately map the network that matches the intricacy of RAS pathway interactions in cancer.


Asunto(s)
Genómica , Terapia Molecular Dirigida , Neoplasias/metabolismo , Neoplasias/terapia , Proteínas ras/metabolismo , Animales , Humanos , Modelos Biológicos , Neoplasias/genética , Neoplasias/patología , Transducción de Señal
9.
Mol Syst Biol ; 12(3): 860, 2016 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-26969729

RESUMEN

The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple genes may influence FBC risk, we hypothesized that a pathway-based strategy examining different data types from multiple tissues could elucidate the biological basis for FBC. In this study, we performed integrated analyses of gene expression and exome-sequencing data from peripheral blood mononuclear cells and showed that cell adhesion pathways are significantly and consistently dysregulated in women who develop FBC. The dysregulation of cell adhesion pathways in high-risk women was also identified by pathway-based profiling applied to normal breast tissue data from two independent cohorts. The results of our genomic analyses were validated in normal primary mammary epithelial cells from high-risk and control women, using cell-based functional assays, drug-response assays, fluorescence microscopy, and Western blotting assays. Both genomic and cell-based experiments indicate that cell-cell and cell-extracellular matrix adhesion processes seem to be disrupted in non-malignant cells of women at high risk for FBC and suggest a potential role for these processes in FBC development.


Asunto(s)
Neoplasias de la Mama/metabolismo , Predisposición Genética a la Enfermedad , Transducción de Señal , Anciano , Neoplasias de la Mama/genética , Neoplasias de la Mama/patología , Adhesión Celular , Estudios de Cohortes , Femenino , Perfilación de la Expresión Génica , Variación Genética , Humanos , Leucocitos Mononucleares/metabolismo , Persona de Mediana Edad
10.
Mol Cell ; 34(1): 104-14, 2009 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-19362539

RESUMEN

Recent studies have emphasized the importance of pathway-specific interpretations for understanding the functional relevance of gene alterations in human cancers. Although signaling activities are often conceptualized as linear events, in reality, they reflect the activity of complex functional networks assembled from modules that each respond to input signals. To acquire a deeper understanding of this network structure, we developed an approach to deconstruct pathways into modules represented by gene expression signatures. Our studies confirm that they represent units of underlying biological activity linked to known biochemical pathway structures. Importantly, we show that these signaling modules provide tools to dissect the complexity of oncogenic states that define disease outcomes as well as response to pathway-specific therapeutics. We propose that this model of pathway structure constitutes a framework to study the processes by which information propogates through cellular networks and to elucidate the relationships of fundamental modules to cellular and clinical phenotypes.


Asunto(s)
Genómica/métodos , Neoplasias/genética , Transducción de Señal/genética , Línea Celular Tumoral , Análisis por Conglomerados , Factores de Transcripción E2F/genética , Factores de Transcripción E2F/metabolismo , Perfilación de la Expresión Génica , Regulación Neoplásica de la Expresión Génica , Humanos , Modelos Genéticos , Neoplasias/metabolismo , Proteínas ras/genética , Proteínas ras/metabolismo
11.
Bioinformatics ; 31(22): 3666-72, 2015 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-26209429

RESUMEN

MOTIVATION: The Cancer Genome Atlas (TCGA) RNA-Sequencing data are used widely for research. TCGA provides 'Level 3' data, which have been processed using a pipeline specific to that resource. However, we have found using experimentally derived data that this pipeline produces gene-expression values that vary considerably across biological replicates. In addition, some RNA-Sequencing analysis tools require integer-based read counts, which are not provided with the Level 3 data. As an alternative, we have reprocessed the data for 9264 tumor and 741 normal samples across 24 cancer types using the Rsubread package. We have also collated corresponding clinical data for these samples. We provide these data as a community resource. RESULTS: We compared TCGA samples processed using either pipeline and found that the Rsubread pipeline produced fewer zero-expression genes and more consistent expression levels across replicate samples than the TCGA pipeline. Additionally, we used a genomic-signature approach to estimate HER2 (ERBB2) activation status for 662 breast-tumor samples and found that the Rsubread data resulted in stronger predictions of HER2 pathway activity. Finally, we used data from both pipelines to classify 575 lung cancer samples based on histological type. This analysis identified various non-coding RNA that may influence lung-cancer histology. AVAILABILITY AND IMPLEMENTATION: The RNA-Sequencing and clinical data can be downloaded from Gene Expression Omnibus (accession number GSE62944). Scripts and code that were used to process and analyze the data are available from https://github.com/srp33/TCGA_RNASeq_Clinical. CONTACT: stephen_piccolo@byu.edu or andreab@genetics.utah.edu SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.


Asunto(s)
Neoplasias de la Mama/genética , Genoma Humano , Análisis de Secuencia de ARN/métodos , Estadística como Asunto , Neoplasias de la Mama/clasificación , Femenino , Regulación Neoplásica de la Expresión Génica , Humanos , Curva ROC , Reproducibilidad de los Resultados
12.
Bioinformatics ; 31(11): 1745-53, 2015 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-25617415

RESUMEN

MOTIVATION: Although gene-expression signature-based biomarkers are often developed for clinical diagnosis, many promising signatures fail to replicate during validation. One major challenge is that biological samples used to generate and validate the signature are often from heterogeneous biological contexts-controlled or in vitro samples may be used to generate the signature, but patient samples may be used for validation. In addition, systematic technical biases from multiple genome-profiling platforms often mask true biological variation. Addressing such challenges will enable us to better elucidate disease mechanisms and provide improved guidance for personalized therapeutics. RESULTS: Here, we present a pathway profiling toolkit, Adaptive Signature Selection and InteGratioN (ASSIGN), which enables robust and context-specific pathway analyses by efficiently capturing pathway activity in heterogeneous sets of samples and across profiling technologies. The ASSIGN framework is based on a flexible Bayesian factor analysis approach that allows for simultaneous profiling of multiple correlated pathways and for the adaptation of pathway signatures into specific disease. We demonstrate the robustness and versatility of ASSIGN in estimating pathway activity in simulated data, cell lines perturbed pathways and in primary tissues samples including The Cancer Genome Atlas breast carcinoma samples and liver samples exposed to genotoxic carcinogens. AVAILABILITY AND IMPLEMENTATION: Software for our approach is available for download at: http://www.bioconductor.org/packages/release/bioc/html/ASSIGN.html and https://github.com/wevanjohnson/ASSIGN.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Programas Informáticos , Animales , Teorema de Bayes , Neoplasias de la Mama/genética , Femenino , Genómica/métodos , Humanos , Ratas , Transducción de Señal/genética
13.
Proc Natl Acad Sci U S A ; 110(44): 17778-83, 2013 Oct 29.
Artículo en Inglés | MEDLINE | ID: mdl-24128763

RESUMEN

Over the past two decades, many biotechnology platforms have been developed for high-throughput gene expression profiling. However, because each platform is subject to technology-specific biases and produces distinct raw-data distributions, researchers have experienced difficulty in integrating data across platforms. Data integration is crucial to data-generating consortiums, researchers transitioning to newer profiling technologies, and individuals seeking to aggregate data across experiments. We address this need with our Universal exPression Code (UPC) approach, which corrects for platform-specific background noise using models that account for the genomic base composition and length of target regions; this approach also uses a mixture model to estimate whether a gene is active in a particular profiling sample. The latter produces standardized UPC values on a zero-to-one scale, so that they can be interpreted consistently, irrespective of profiling technology, thus enabling downstream analysis pipelines to be developed in a platform-agnostic manner. The UPC method can be applied to one- and two-channel expression microarrays and to next-generation sequencing data (RNA sequencing). Furthermore, UPCs are derived using information from within a given sample only--no ancillary samples are required at processing time. Thus, UPCs are suitable for personalized-medicine workflows where samples must be processed individually rather than in batches. In a variety of analyses and comparisons, UPCs perform comparably to other methods designed specifically for microarrays or RNA sequencing in most settings. Software for calculating UPCs is freely available at www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html.


Asunto(s)
Algoritmos , Código de Barras del ADN Taxonómico/métodos , Perfilación de la Expresión Génica/métodos , Genes/genética , Modelos Genéticos , Programas Informáticos , Activación Transcripcional/fisiología , Composición de Base
14.
Nat Rev Cancer ; 6(9): 735-41, 2006 09.
Artículo en Inglés | MEDLINE | ID: mdl-16915294

RESUMEN

The accumulation of multiple mutations and alterations in the cancer genome underlies the complexity of cancer phenotypes. A consequence of these alterations is the deregulation of various cell-signalling pathways that control cell function. Molecular-profiling studies, particularly DNA microarray analyses, have the potential to describe this complexity. These studies also provide an opportunity to link pathway deregulation with potential therapeutic strategies. This approach, when coupled with other methods for identifying pathway activation, provides an opportunity to both match individual patients with the most appropriate therapeutic strategy and identify potential options for combination therapy.


Asunto(s)
Neoplasias/terapia , Oncogenes/fisiología , Transducción de Señal , Animales , Humanos
15.
Breast Cancer Res ; 16(2): R36, 2014 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-24708766

RESUMEN

INTRODUCTION: Triple-negative breast cancer (TNBC) is aggressive and lacks targeted therapies. Phosphatidylinositide 3-kinase (PI3K)/mammalian target of rapamycin (mTOR) pathways are frequently activated in TNBC patient tumors at the genome, gene expression and protein levels, and mTOR inhibitors have been shown to inhibit growth in TNBC cell lines. We describe a panel of patient-derived xenografts representing multiple TNBC subtypes and use them to test preclinical drug efficacy of two mTOR inhibitors, sirolimus (rapamycin) and temsirolimus (CCI-779). METHODS: We generated a panel of seven patient-derived orthotopic xenografts from six primary TNBC tumors and one metastasis. Patient tumors and corresponding xenografts were compared by histology, immunohistochemistry, array comparative genomic hybridization (aCGH) and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) sequencing; TNBC subtypes were determined. Using a previously published logistic regression approach, we generated a rapamycin response signature from Connectivity Map gene expression data and used it to predict rapamycin sensitivity in 1,401 human breast cancers of different intrinsic subtypes, prompting in vivo testing of mTOR inhibitors and doxorubicin in our TNBC xenografts. RESULTS: Patient-derived xenografts recapitulated histology, biomarker expression and global genomic features of patient tumors. Two primary tumors had PIK3CA coding mutations, and five of six primary tumors showed flanking intron single nucleotide polymorphisms (SNPs) with conservation of sequence variations between primary tumors and xenografts, even on subsequent xenograft passages. Gene expression profiling showed that our models represent at least four of six TNBC subtypes. The rapamycin response signature predicted sensitivity for 94% of basal-like breast cancers in a large dataset. Drug testing of mTOR inhibitors in our xenografts showed 77 to 99% growth inhibition, significantly more than doxorubicin; protein phosphorylation studies indicated constitutive activation of the mTOR pathway that decreased with treatment. However, no tumor was completely eradicated. CONCLUSIONS: A panel of patient-derived xenograft models covering a spectrum of TNBC subtypes was generated that histologically and genomically matched original patient tumors. Consistent with in silico predictions, mTOR inhibitor testing in our TNBC xenografts showed significant tumor growth inhibition in all, suggesting that mTOR inhibitors can be effective in TNBC, but will require use with additional therapies, warranting investigation of optimal drug combinations.


Asunto(s)
Antineoplásicos/uso terapéutico , Serina-Treonina Quinasas TOR/antagonistas & inhibidores , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Ensayos Antitumor por Modelo de Xenoinjerto/métodos , Animales , Western Blotting , Línea Celular Tumoral , Fosfatidilinositol 3-Quinasa Clase I , Hibridación Genómica Comparativa , Análisis Mutacional de ADN , Doxorrubicina/uso terapéutico , Femenino , Regulación Neoplásica de la Expresión Génica/efectos de los fármacos , Humanos , Inmunohistoquímica , Células MCF-7 , Ratones , Mutación , Análisis de Secuencia por Matrices de Oligonucleótidos , Fosfatidilinositol 3-Quinasas/genética , Fosforilación/efectos de los fármacos , Proteínas Quinasas S6 Ribosómicas 70-kDa/genética , Proteínas Quinasas S6 Ribosómicas 70-kDa/metabolismo , Sirolimus/análogos & derivados , Sirolimus/uso terapéutico , Serina-Treonina Quinasas TOR/genética , Serina-Treonina Quinasas TOR/metabolismo , Transcriptoma/efectos de los fármacos , Neoplasias de la Mama Triple Negativas/genética , Neoplasias de la Mama Triple Negativas/metabolismo
16.
N Engl J Med ; 364(12): 1176, 2011 Mar 24.
Artículo en Inglés | MEDLINE | ID: mdl-21366430

RESUMEN

To the Editor: We would like to retract our article, "A Genomic Strategy to Refine Prognosis in Early-Stage Non-Small-Cell Lung Cancer,"(1) which was published in the Journal on August 10, 2006. Using a sample set from a study by the American College of Surgeons Oncology Group (ACOSOG) and a collection of samples from a study by the Cancer and Leukemia Group B (CALGB), we have tried and failed to reproduce results supporting the validation of the lung metagene model described in the article. We deeply regret the effect of this action on the work of other investigators.

17.
Am J Respir Crit Care Med ; 187(9): 933-42, 2013 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-23471465

RESUMEN

RATIONALE: Molecular phenotyping of chronic obstructive pulmonary disease (COPD) has been impeded in part by the difficulty in obtaining lung tissue samples from individuals with impaired lung function. OBJECTIVES: We sought to determine whether COPD-associated processes are reflected in gene expression profiles of bronchial airway epithelial cells obtained by bronchoscopy. METHODS: Gene expression profiling of bronchial brushings obtained from 238 current and former smokers with and without COPD was performed using Affymetrix Human Gene 1.0 ST Arrays. MEASUREMENTS AND MAIN RESULTS: We identified 98 genes whose expression levels were associated with COPD status, FEV1% predicted, and FEV1/FVC. In silico analysis identified activating transcription factor 4 (ATF4) as a potential transcriptional regulator of genes with COPD-associated airway expression, and ATF4 overexpression in airway epithelial cells in vitro recapitulates COPD-associated gene expression changes. Genes with COPD-associated expression in the bronchial airway epithelium had similarly altered expression profiles in prior studies performed on small-airway epithelium and lung parenchyma, suggesting that transcriptomic alterations in the bronchial airway epithelium reflect molecular events found at more distal sites of disease activity. Many of the airway COPD-associated gene expression changes revert toward baseline after therapy with the inhaled corticosteroid fluticasone in independent cohorts. CONCLUSIONS: Our findings demonstrate a molecular field of injury throughout the bronchial airway of active and former smokers with COPD that may be driven in part by ATF4 and is modifiable with therapy. Bronchial airway epithelium may ultimately serve as a relatively accessible tissue in which to measure biomarkers of disease activity for guiding clinical management of COPD.


Asunto(s)
Factor de Transcripción Activador 4/genética , Bronquios/metabolismo , Células Epiteliales/metabolismo , Enfermedad Pulmonar Obstructiva Crónica/genética , Fumar/efectos adversos , Transcriptoma/fisiología , Anciano , Análisis de Varianza , Androstadienos , Bronquios/efectos de los fármacos , Broncodilatadores/farmacología , Broncoscopía , Células Epiteliales/efectos de los fármacos , Femenino , Fluticasona , Humanos , Masculino , Persona de Mediana Edad , Enfermedad Pulmonar Obstructiva Crónica/tratamiento farmacológico , Enfermedad Pulmonar Obstructiva Crónica/metabolismo , Reacción en Cadena en Tiempo Real de la Polimerasa , Pruebas de Función Respiratoria , Transcriptoma/efectos de los fármacos
18.
bioRxiv ; 2024 Sep 06.
Artículo en Inglés | MEDLINE | ID: mdl-39282402

RESUMEN

Chemotherapy remains a commonly used and important treatment option for metastatic breast cancer. A majority of ER+ metastatic breast cancer patients ultimately develop resistance to chemotherapy, resulting in disease progression. We hypothesized that an "evolutionary double-bind", where treatment with one drug improves the response to a different agent, would improve the effectiveness and durability of responses to chemotherapy. This approach exploits vulnerabilities in acquired resistance mechanisms. Evolutionary models can be used in refractory cancer to identify alternative treatment strategies that capitalize on acquired vulnerabilities and resistance traits for improved outcomes. To develop and test these models, ER+ breast cancer cell lineages sensitive and resistant to chemotherapy are grown in spheroids with varied initial population frequencies to measure cross-sensitivity and efficacy of chemotherapy and add-on treatments such as disulfiram combination treatment. Different treatment schedules then assessed the best strategy for reducing the selection of resistant populations. We developed and parameterized a game-theoretic mathematical model from this in vitro experimental data, and used it to predict the existence of a double-bind where selection for resistance to chemotherapy induces sensitivity to disulfiram. The model predicts a dose-dependent re-sensitization (a double-bind) to chemotherapy for monotherapy disulfiram.

19.
Nat Med ; 12(11): 1294-300, 2006 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-17057710

RESUMEN

Using in vitro drug sensitivity data coupled with Affymetrix microarray data, we developed gene expression signatures that predict sensitivity to individual chemotherapeutic drugs. Each signature was validated with response data from an independent set of cell line studies. We further show that many of these signatures can accurately predict clinical response in individuals treated with these drugs. Notably, signatures developed to predict response to individual agents, when combined, could also predict response to multidrug regimens. Finally, we integrated the chemotherapy response signatures with signatures of oncogenic pathway deregulation to identify new therapeutic strategies that make use of all available drugs. The development of gene expression profiles that can predict response to commonly used cytotoxic agents provides opportunities to better use these drugs, including using them in combination with existing targeted therapies.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Genoma Humano , Taxoides/uso terapéutico , Protocolos de Quimioterapia Combinada Antineoplásica/administración & dosificación , Línea Celular Tumoral , Docetaxel , Expresión Génica , Humanos , Farmacogenética , Taxoides/administración & dosificación
20.
Genomics ; 100(6): 337-44, 2012 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-22959562

RESUMEN

Gene-expression microarrays allow researchers to characterize biological phenomena in a high-throughput fashion but are subject to technological biases and inevitable variabilities that arise during sample collection and processing. Normalization techniques aim to correct such biases. Most existing methods require multiple samples to be processed in aggregate; consequently, each sample's output is influenced by other samples processed jointly. However, in personalized-medicine workflows, samples may arrive serially, so renormalizing all samples upon each new arrival would be impractical. We have developed Single Channel Array Normalization (SCAN), a single-sample technique that models the effects of probe-nucleotide composition on fluorescence intensity and corrects for such effects, dramatically increasing the signal-to-noise ratio within individual samples while decreasing variation across samples. In various benchmark comparisons, we show that SCAN performs as well as or better than competing methods yet has no dependence on external reference samples and can be applied to any single-channel microarray platform.


Asunto(s)
Perfilación de la Expresión Génica/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Medicina de Precisión/métodos , Análisis de Varianza , Fluorescencia , Ensayos Analíticos de Alto Rendimiento/métodos , Humanos , Tamaño de la Muestra , Sesgo de Selección , Relación Señal-Ruido , Flujo de Trabajo
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