Computational modeling to elucidate molecular mechanisms of epigenetic memory

How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes differentiate reproducibly from a single fertilized egg? These are fundamental problems in developmental biology. Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. The complexity comes partly from the number of molecular species and the broad time scales involved. In recent years mathematical modeling has made significant contributions on elucidating the molecular mechanisms of DNA methylation and histone covalent modification inheritance. We will pedagogically introduce the typical procedure and some technical details of performing a mathematical modeling study, and discuss future developments.Comment: 36 pages, 4 figures, 2 tables, book chapte

Aurora kinase A drives the evolution of resistance to third-generation EGFR inhibitors in lung cancer.

Although targeted therapies often elicit profound initial patient responses, these effects are transient due to residual disease leading to acquired resistance. How tumors transition between drug responsiveness, tolerance and resistance, especially in the absence of preexisting subclones, remains unclear. In epidermal growth factor receptor (EGFR)-mutant lung adenocarcinoma cells, we demonstrate that residual disease and acquired resistance in response to EGFR inhibitors requires Aurora kinase A (AURKA) activity. Nongenetic resistance through the activation of AURKA by its coactivator TPX2 emerges in response to chronic EGFR inhibition where it mitigates drug-induced apoptosis. Aurora kinase inhibitors suppress this adaptive survival program, increasing the magnitude and duration of EGFR inhibitor response in preclinical models. Treatment-induced activation of AURKA is associated with resistance to EGFR inhibitors in vitro, in vivo and in most individuals with EGFR-mutant lung adenocarcinoma. These findings delineate a molecular path whereby drug resistance emerges from drug-tolerant cells and unveils a synthetic lethal strategy for enhancing responses to EGFR inhibitors by suppressing AURKA-driven residual disease and acquired resistance

Emisión de metano en ovinos alimentados con Pennisetum purpureum y árboles que contienen taninos condensados

El objetivo fue evaluar el efecto de los taninos condensados (TC) contenidos en el follaje de arbóreas tropicales, sobre el consumo de materia seca y orgánica (CMS, CMO), la digestibilidad de la materia seca (DMS) y emisiones de metano (CH4) en ovinos alimentados con una ración basal de pasto Pennisetum purpureum. Cuatro ovinos de pelo con un peso vivo promedio de 21.6±2.0 kg se sometieron a cuatro tratamientos en un diseño cuadro latino 4 x 4. Los tratamientos fueron P. purpureum (PP), P. purpureum + Havardia albicans (PPHA), P. purpureum + Bursera simaruba (PPBS), y P. purpureum + Acacia pennatula (PPAP); el follaje de las arbóreas se incluyó en 300 g/kg de MS de la ración. El consumo, la digestibilidad y la producción total de metano entérico se midieron por periodos de 23 h. La producción de metano se midió en cajas de respiración de circuito abierto. El consumo y digestibilidad de la MS y materia orgánica (MO) entre los tratamientos PP, PPHA, PPBS y PPAP no se afectaron por la inclusión de los follajes de arbóreas en la ración (P>0.05). Cuando la producción de CH4 se expresó en L/kg del CMS, CMO o consumo de fibra detergente neutro los resultados fueron similares entre tratamientos (PP, PPHA, PPBS y PPAP) (P>0.05). Se concluye que los TC contenidos en el follaje de Havardia albicans, Acacia pennatula y Bursera simaruba no afectaron las emisiones de CH4 al nivel de incorporación de 30 % de la MS; tampoco se observaron efectos en el CMS, CMO, DMS y concentración molar de ácidos grasos volátiles

IL-2 receptor γ chain cytokines differentially regulate human CD8+CD127+ and CD8+CD127− T cell division and susceptibility to apoptosis

Expression of IL-7 receptor α (CD127) is associated with naive and memory (i.e. non-effector) CD8+ T cell phenotypes. Effector CD8+ T cells are predominantly CD127− and most die by apoptosis. Therefore, CD127 appears to be a marker for CD8+ T cell differentiation, yet its role in CD8+ T cell survival and memory development is unclear. To address this, we investigated the cell death and cell division of isolated CD8+CD127+ and CD8+CD127− T cells in response to common IL-2 receptor γ chain (γC) cytokines other than IL-7. We show here that (i) memory cells (CD127+CD45RA−) divide frequently in response to either IL-2, -4 or -15; (ii) IL-2 and -15 enhance cell division in effector–memory-like cells (CD127−CD45RA+) while IL-4 enhances the cell division of effector cells (CD127−CD45RA−); (iii) CD8+CD127+ T cells are more sensitive to the anti-apoptotic effects of IL-2 or IL-15 than CD8+CD127− T cells and (iv) CD8+CD127+ T cell produce more Bcl-2 in response to IL-2 or IL-15 compared with CD8+CD127− T cells. Therefore, CD8+CD127+ and CD8+CD127− T cells differ in their responsiveness to cell division and anti-apoptotic signals from IL-2, -4 and -15. This suggests a role for γC cytokines in the pathogenesis of diseases in which CD127 expression is altered on CD8+ T cells such as in progressive viral infections and cancer

LSST: from Science Drivers to Reference Design and Anticipated Data Products

(Abridged) We describe here the most ambitious survey currently planned in the optical, the Large Synoptic Survey Telescope (LSST). A vast array of science will be enabled by a single wide-deep-fast sky survey, and LSST will have unique survey capability in the faint time domain. The LSST design is driven by four main science themes: probing dark energy and dark matter, taking an inventory of the Solar System, exploring the transient optical sky, and mapping the Milky Way. LSST will be a wide-field ground-based system sited at Cerro Pach\'{o}n in northern Chile. The telescope will have an 8.4 m (6.5 m effective) primary mirror, a 9.6 deg$^2$ field of view, and a 3.2 Gigapixel camera. The standard observing sequence will consist of pairs of 15-second exposures in a given field, with two such visits in each pointing in a given night. With these repeats, the LSST system is capable of imaging about 10,000 square degrees of sky in a single filter in three nights. The typical 5$\sigma$ point-source depth in a single visit in $r$ will be $\sim 24.5$ (AB). The project is in the construction phase and will begin regular survey operations by 2022. The survey area will be contained within 30,000 deg$^2$ with $\delta<+34.5^\circ$, and will be imaged multiple times in six bands, $ugrizy$, covering the wavelength range 320--1050 nm. About 90\% of the observing time will be devoted to a deep-wide-fast survey mode which will uniformly observe a 18,000 deg$^2$ region about 800 times (summed over all six bands) during the anticipated 10 years of operations, and yield a coadded map to $r\sim27.5$. The remaining 10\% of the observing time will be allocated to projects such as a Very Deep and Fast time domain survey. The goal is to make LSST data products, including a relational database of about 32 trillion observations of 40 billion objects, available to the public and scientists around the world.Comment: 57 pages, 32 color figures, version with high-resolution figures available from https://www.lsst.org/overvie

Heterogeneity in Health Insurance Coverage Among US Latino Adults

We sought to determine the differences in observed and unobserved factors affecting rates of health insurance coverage between US Latino adults and US Latino adults of Mexican ancestry. Our hypothesis was that Latinos of Mexican ancestry have worse health insurance coverage than their non-Mexican Latino counterparts. The National Health Interview Survey (NHIS) database from 1999–2007 consists of 33,847 Latinos. We compared Latinos of Mexican ancestry to non-Mexican Latinos in the initial descriptive analysis of health insurance coverage. Disparities in health insurance coverage across Latino categories were later analyzed in a multivariable logistic regression framework, which adjusts for confounding variables. The Blinder-Oaxaca technique was applied to parse out differences in health insurance coverage into observed and unobserved components. US Latinos of Mexican ancestry consistently had lower rates of health insurance coverage than did US non-Mexican Latinos. Approximately 65% of these disparities can be attributed to differences in observed characteristics of the Mexican ancestry population in the US (e.g., age, sex, income, employment status, education, citizenship, language and health condition). The remaining disparities may be attributed to unobserved heterogeneity that may include unobserved employment-related information (e.g., type of employment and firm size) and behavioral and idiosyncratic factors (e.g., risk aversion and cultural differences). This study confirmed that Latinos of Mexican ancestry were less likely to have health insurance than were non-Mexican Latinos. Moreover, while differences in observed socioeconomic and demographic factors accounted for most of these disparities, the share of unobserved heterogeneity accounted for 35% of these differences

Secondary cytogenetic abnormalities in core-binding factor AML harboring inv(16) vs t(8;21)

Patients with core-binding factor (CBF) acute myeloid leukemia (AML), caused by either t(8; 21)(q22;q22) or inv(16)(p13q22)/t(16;16)(p13;q22), have higher complete remission rates and longer survival than patients with other subtypes of AML. However, similar to 40% of patients relapse, and the literature suggests that patients with inv(16) fare differently from those with t(8;21). We retrospectively analyzed 537 patients with CBF-AML, focusing on additional cytogenetic aberrations to examine their impact on clinical outcomes. Trisomies of chromosomes 8, 21, or 22 were significantly more common in patients with inv(16)/t(16;16): 16% vs 7%, 6% vs 0%, and 17% vs 0%, respectively. In contrast, del(9q) and loss of a sex chromosome were more frequent in patients with t(8;21): 15% vs 0.4% for del(9q), 37% vs 0% for loss of X in females, and 44% vs 5% for loss of Y in males. Hyperdiploidy was more frequent in patients with inv(16) (25% vs 9%, whereas hypodiploidy was more frequent in patients with t(8;21) (37% vs 3%. In multivariable analyses (adjusted for age, white blood counts at diagnosis, and KIT mutation status), trisomy 8 was associated with improved overall survival (OS) in inv(16), whereas the presence of other chromosomal abnormalities (not trisomy 8) was associated with decreased OS. In patients with t(8;21), hypodiploidy was associated with improved disease-free survival; hyperdiploidy and del(9q) were associated with improved OS. KIT mutation (either positive or not tested, compared with negative) conferred poor prognoses in univariate analysis only in patients with t(8;21)

Emerging roles of ATF2 and the dynamic AP1 network in cancer

Cooperation among transcription factors is central for their ability to execute specific transcriptional programmes. The AP1 complex exemplifies a network of transcription factors that function in unison under normal circumstances and during the course of tumour development and progression. This Perspective summarizes our current understanding of the changes in members of the AP1 complex and the role of ATF2 as part of this complex in tumorigenesis.Fil: Lopez Bergami, Pablo Roberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental (i); Argentina; ArgentinaFil: Lau, Eric . Burnham Institute for Medical Research; Estados UnidosFil: Ronai, Zeev . Burnham Institute for Medical Research; Estados Unido