Induction of Stable Drug Resistance in Human Breast Cancer Cells Using a Combinatorial Zinc Finger Transcription Factor Library

Combinatorial libraries of artificial zinc-finger transcription factors (ZF-TFs) provide a robust tool for inducing and understanding various functional components of the cancer phenotype. Herein, we utilized combinatorial ZF-TF library technology to better understand how breast cancer cells acquire resistance to fulvestrant, a clinically important anti-endocrine therapeutic agent. From a diverse collection of nearly 400,000 different ZF-TFs, we isolated six ZF-TF library members capable of inducing stable, long-term anti-endocrine drug-resistance in two independent estrogen receptor-positive breast cancer cell lines. Comparative gene expression profile analysis of the six different ZF-TF-transduced breast cancer cell lines revealed five distinct clusters of differentially expressed genes. One cluster was shared among all 6 ZF-TF-transduced cell lines and therefore constituted a common fulvestrant-resistant gene expression signature. Pathway enrichment-analysis of this common fulvestrant resistant signature also revealed significant overlap with gene sets associated with an estrogen receptor-negative-like state and with gene sets associated with drug resistance to different classes of breast cancer anti-endocrine therapeutic agents. Enrichment-analysis of the four remaining unique gene clusters revealed overlap with myb-regulated genes. Finally, we also demonstrated that the common fulvestrant-resistant signature is associated with poor prognosis by interrogating five independent, publicly available human breast cancer gene expression datasets. Our results demonstrate that artificial ZF-TF libraries can be used successfully to induce stable drug-resistance in human cancer cell lines and to identify a gene expression signature that is associated with a clinically relevant drug-resistance phenotype

Systematic Bias in Genomic Classification Due to Contaminating Non-neoplastic Tissue in Breast Tumor Samples

Abstract Background Genomic tests are available to predict breast cancer recurrence and to guide clinical decision making. These predictors provide recurrence risk scores along with a measure of uncertainty, usually a confidence interval. The confidence interval conveys random error and not systematic bias. Standard tumor sampling methods make this problematic, as it is common to have a substantial proportion (typically 30-50%) of a tumor sample comprised of histologically benign tissue. This "normal" tissue could represent a source of non-random error or systematic bias in genomic classification. Methods To assess the performance characteristics of genomic classification to systematic error from normal contamination, we collected 55 tumor samples and paired tumor-adjacent normal tissue. Using genomic signatures from the tumor and paired normal, we evaluated how increasing normal contamination altered recurrence risk scores for various genomic predictors. Results Simulations of normal tissue contamination caused misclassification of tumors in all predictors evaluated, but different breast cancer predictors showed different types of vulnerability to normal tissue bias. While two predictors had unpredictable direction of bias (either higher or lower risk of relapse resulted from normal contamination), one signature showed predictable direction of normal tissue effects. Due to this predictable direction of effect, this signature (the PAM50) was adjusted for normal tissue contamination and these corrections improved sensitivity and negative predictive value. For all three assays quality control standards and/or appropriate bias adjustment strategies can be used to improve assay reliability. Conclusions Normal tissue sampled concurrently with tumor is an important source of bias in breast genomic predictors. All genomic predictors show some sensitivity to normal tissue contamination and ideal strategies for mitigating this bias vary depending upon the particular genes and computational methods used in the predictor

Aportes de los viviendistas colombianos a la paz en el posacuerdo: un ejercicio de Investigación Acción Participativa con fundadores barriales

Este artículo sintetiza una tesis del Doctorado en Estudios Políticos elaborada a partir de la metodología de Investigación Acción Participativa (iap). Esa investigación reconstruye las memorias de una organización social de viviendistas que ha funcionado durante 58 años en América Latina, a pesar de la persecución estatal y de sus dificultades internas; ilustra el trasegar del despojo, el destierro y la lucha por la vivienda de millones de colombianos y contribuye a promover la no repetición indispensable para una paz duradera. Consecuente con la opción metodológica de la iap, la tesis refleja una construcción colectiva, con veteranas fundadoras de los barrios y directivos de la Central Provivienda Nacional (Cenaprov), organización que representa la historia de cerca de cien mil familias destechadas que lograron ser propietarias de sus viviendas. Esta es una experiencia social basada en acciones colectivas autogestionarias que fue silenciada por el pensamiento hegemónico, pero que ha sido reconstruida con sus protagonistas, a partir de una reflexión compartida, orientada a comprender sus dinámicas internas y algunas circunstancias que influyeron en la organización y en los cambios desde su origen hasta sus perspectivas en el postacuerdo. Con algunas particularidades, esta experiencia es un ejemplo de un largo proceso organizativo de colonos destechados que solidariamente superaron el desarraigo,lograron formarse una identidad barrial y soñar con mejores perspectivas de vida ciudadana. El argumento central es que en los barrios populares fundados por los colonos deCenaprov se intentó consolidar un nuevo modelo barrial, solidario y autogestionario. A través de la resistencia a la violencia estatal, la mayoría de los fundadores sobrevivienteshan preservado su dignidad personal como sujetos políticos. A pesar de la permanente estigmatización, transmiten su experiencia a las nuevas generaciones, continúan con proyectosalternativos en la perspectiva de los postacuerdos y sueñan con una paz estable, duradera y con justicia social.This article synthesizes a Political Studies doctorate thesis based on Participatory Action Research (par) methodology. The study reconstructs the memories of a housing activist organization which has operated for 58 years in Latin America in spite of state persecution and internal difficulties. The article illustrates the eviction, dispossession, uprootedness and the struggle for housing of millions of Colombians and promotes the non-repetition of this scenario for a lasting peace. In line with the par methodology, the thesis looks at a collective construction with neighborhood founders and directors of the Central Provivienda Nacional (Cenaprov), an organization that represents the history of 100,000 families without homes that were able to become owners of their homes. This is a social experience based on self-managed collective actions that was silenced by hegemonic thought. Nevertheless, it has been reconstructed by its actors through a shared reflection to understand the internal dynamics as well as some circumstances that influenced the organization from its origin, with perspectives on the post-agreement. With some particularities, this experience is an example of a long organizational process by homeless settlers who collectively overcame uprootedness to form a neighborhood identity and dream of a better daily life. The central argument is that the neighborhoods founded by the Cenaprov settlerswere based on a new, solidary and self-managed neighborhood model. Through resistance to state violence, most of the surviving founders have preserved their personal dignity as political subjects. Despite continuous stigmatization, they transmit their experience to the new generations, continue with alternative projects in the framework of the post-agreement and dream of a lasting and stable peace with social justice.Este artigo sintetiza uma tese de doutoramento em Estudos Políticos elaborada a partir da metodologia de Pesquisa-Ação Participativa (pap). Esta pesquisa reconstrói as memórias de uma organização social de moradias que vem funcionando há 58 anos na América Latina, apesar da persecução estatal e de suas dificuldades internas; ilustra o movimento de despojamento, o desterro e a luta pela moradia de milhares de colombianos, e contribui para promover a não repetição indispensável para uma paz duradoura. Consequente com a opção metodológica da pap, a tese reflete uma construção coletiva, com fundadoras dos bairros veteranas e diretores da Central Provivienda Nacional (Cenaprov), organização que representa a história de cerca de 100 mil famílias desterradas que conseguiram ser proprietárias de suas habitações. Esta é uma experiência social baseada em ações coletivas autogestionadas, que foi silenciada pelo pensamento hegemônico, mas que tem sido reconstruída com seus protagonistas, a partir de uma reflexão partilhada,orientada a compreender suas dinâmicas internas e algumas circunstâncias que influenciaram na organização e nas mudanças desde sua origem até suas perspectivas nopós-acordo. Com algumas particularidades, essa experiência é um exemplo de um longo processo organizativo de colonos desterrados que solidariamente superaram o desenraizamento,conseguiram formar uma identidade de bairro e sonhar com melhores perspectivas de vida cidadã. Argumenta-se que, nos bairros populares fundados pelos colonos de Cenaprov, tentou-se consolidar um novo modelo de bairro, solidário e autogestionado. Por meio da resistência à violência estatal, a maioria dos fundadores sobreviventes preservou sua dignidade pessoal como sujeitos políticos. Embora a permanente estigmatização, transmitem sua experiência às novas gerações, continuam com projetos alternativos na perspectiva do pós-acordo e sonham com uma paz estável, duradoura e com justiça socia

Using a gene expression signature when controversy exists regarding the indication for adjuvant systemic treatment reduces the proportion of patients receiving adjuvant chemotherapy : a nationwide study

PURPOSE: The Dutch national guideline advises use of gene-expression signatures, such as the 70-gene signature (70-GS), in case of ambivalence regarding the benefit of adjuvant chemotherapy (CT). In this nationwide study, the impact of 70-GS use on the administration of CT in early breast cancer patients with a dubious indication for CT is assessed. METHODS: Patients within a national guideline directed indication area for 70-GS use who were surgically treated between November 2011 and April 2013 were selected from the Netherlands Cancer Registry database. The effect of 70-GS use on the administration of CT was evaluated in guideline- and age-delineated subgroups addressing potential effect of bias by linear mixed-effect modeling and instrumental variable (IV) analyses. RESULTS: A total of 2,043 patients within the indicated area for 70-GS use were included, of whom 298 received a 70-GS. Without use of the 70-GS, 45% of patients received CT. The 70-GS use was associated with a 9.5% decrease in CT administration (95% confidence interval (CI): -15.7 to -3.3%) in linear mixed-effect model analyses and IV analyses showed similar results (-9.9%; 95% CI: -19.3 to -0.4). CONCLUSION: In patients in whom the Dutch national guidelines suggest the use of a gene-expression profile, 70-GS use is associated with a 10% decrease in the administration of adjuvant CT.Genet Med 18 7, 720-726.Genetics in Medicine (2016); 18 7, 720-726. doi:10.1038/gim.2015.152