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SUMMARYBACKGROUNDAnalysis of sequenced genomes from large three-generation families allows de novo mutations identified in Generation II individuals to be attributed to each of their parents’ germlines in Generation I. Because germline mutations increase with age, we hypothesized that they directly limit the duration of childbearing in women, and if correlated with mutation accumulation in somatic tissues, also reflect systemic aging in both sexes. Here we test whether the germline mutation rates of Generation I individuals when they were young adults predict their remaining survival, as well as the women’s reproductive lifespans.METHODSGermline autosomal mutation counts in 122 Generation I individuals (61 women, 61 men) from 41 three-generation Utah CEPH families were converted to germline mutation rates by normalizing each subject’s number of mutations to the callable portion of their genome. Age at death, cause of death, all-site cancer incidence, and reproductive histories were provided by the Utah Population Database, Cancer Registry, and Utah Genetic Reference Project. Fertility analyses were restricted to the 53 women whose age at last birth (ALB) was at least 30 years, the approximate age when the decline in female fertility begins. Cox proportional hazard regression models were used to test the association of age-adjusted mutation rates (AAMRs) with aging-related outcomes. Linear regression analysis was used to estimate the age when adult germline mutation accumulation rates are established.FINDINGSQuartiles of increasing AAMRs were associated with increasing all-cause mortality rates in both sexes combined (test for trend, p=0.009); subjects in the top quartile of AAMRs experienced more than twice the mortality of bottom quartile subjects (hazard ratio [HR], 2.07; 95% confidence interval [CI], 1.21-3.56; p=0.008; median survival difference = 4.7 years). Women with higher AAMRs had significantly fewer live births and a younger ALB. The analyses also indicate that adult germline mutation accumulation rates are established in adolescence, and that later menarche in women may delay mutation accumulation.INTERPRETATIONParental-age-adjusted germline mutation rates in healthy young adults may provide a measure of both reproductive and systemic aging. Puberty may induce the establishment of adult mutation accumulation rates, just when DNA repair genes’ expression levels are known to begin their lifelong decline.FUNDINGNIH R01AG038797 and R21AG054962 (to R.M.C.); University of Utah Program in Personalized Health (to H.D.M.); NIH T32GM007464 (to T.A.S.); NIH R01AG022095 (to K.R.S.); NIH R01HG006693, R01HG009141, and R01GM124355 (to A.R.Q.); NIH GM118335 and GM059290 (to L.B.J.); NIH P30CA2014 (to the Utah Population Database, a.k.a. the UPDB); National Center for Research Resources Public Health Services grant M01RR00064 (to the Huntsman General Clinical Research Center, University of Utah); National Center for Advancing Translational Sciences NIH grant UL1TR002538 (to the University of Utah’s Center for Clinical and Translational Science); Howard Hughes Medical Institute funding (to Ray White); gifts from the W.M. Keck Foundation (to Stephen M. Prescott and M.F.L.) and from the George S. and Delores Doré Eccles Foundation (to the University of Utah) that supported the Utah Genetic Reference Project (UGRP). Sequencing of the CEPH samples was funded by the Utah Genome Project, the George S. and Dolores Doré Eccles Foundation, and the H.A. and Edna Benning Foundation. We thank the Pedigree and Population Resource of the Huntsman Cancer Institute, University of Utah (funded in part by the Huntsman Cancer Foundation) for its role in the ongoing collection, maintenance and support of the UPDB.

We propose a new penalized method for variable selection and estimation that explicitly incorporates the correlation patterns among predictors. This method is based on a combination of the minimax concave penalty and Laplacian quadratic associated with a graph as the penalty function. We call it the sparse Laplacian shrinkage (SLS) method. The SLS uses the minimax concave penalty for encouraging sparsity and Laplacian quadratic penalty for promoting smoothness among coefficients associated with the correlated predictors. The SLS has a generalized grouping property with respect to the graph represented by the Laplacian quadratic. We show that the SLS possesses an oracle property in the sense that it is selection consistent and equal to the oracle Laplacian shrinkage estimator with high probability. This result holds in sparse, high-dimensional settings with p >> n under reasonable conditions. We derive a coordinate descent algorithm for computing the SLS estimates. Simulation studies are conducted to evaluate the performance of the SLS method and a real data example is used to illustrate its application. Published in at http://dx.doi.org/10.1214/11-AOS897 the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)

AbstractBACKGROUNDTargeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients’ treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors. To determine the dynamics of these molecular changes, we obtained high throughput omics data weekly during the development of cetuximab resistance in a head and neck cancerin vitromodel.RESULTSAn unsupervised algorithm, CoGAPS, was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically.CONCLUSIONSGenes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize resistance. These genes includeFGFR1,which was associated with EGFR inhibitor resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. Our findings provide a relevant towards better understanding of the time course progression of changes resulting in acquired resistance to targeted therapies. This is an important contribution to the development of alternative treatment strategies that would introduce new drugs before the resistant phenotype develops.

Abstract Background Entamoeba histolytica is a significant cause of disease worldwide. However, little is known about the genetic diversity of the parasite. We re-sequenced the genomes of ten laboratory cultured lines of the eukaryotic pathogen Entamoeba histolytica in order to develop a picture of genetic diversity across the genome. Results The extreme nucleotide composition bias and repetitiveness of the E. histolytica genome provide a challenge for short-read mapping, yet we were able to define putative single nucleotide polymorphisms in a large portion of the genome. The results suggest a rather low level of single nucleotide diversity, although genes and gene families with putative roles in virulence are among the more polymorphic genes. We did observe large differences in coverage depth among genes, indicating differences in gene copy number between genomes. We found evidence indicating that recombination has occurred in the history of the sequenced genomes, suggesting that E. histolytica may reproduce sexually. Conclusions E. histolytica displays a relatively low level of nucleotide diversity across its genome. However, large differences in gene family content and gene copy number are seen among the sequenced genomes. The pattern of polymorphism indicates that E. histolytica reproduces sexually, or has done so in the past, which has previously been suggested but not proven.

IL-2 is a cytokine released from CD4+T cells with dual actions and can either potentiate the inflammatory response or quell a chronic inflammatory response depending on its circulating concentration. IL-2 is elevated in many chronic inflammatory conditions and is increased during preeclampsia (PE). PE is characterized by new-onset hypertension during pregnancy and organ dysfunction and increasing evidence indicates that proinflammatory cytokines cause hypertension and mitochondrial (mt) dysfunction during pregnancy. The reduced uterine perfusion pressure (RUPP) model of placental ischemia is a rat model of PE that we commonly use in our laboratory and we have previously shown that low doses of recombinant IL-2 can decrease blood pressure in RUPP rats. The objective of this study was to determine the effects of a low dose of recombinant IL-2 on multi-organ mt dysfunction in the RUPP rat model of PE. We tested our hypothesis by infusing recombinant IL-2 (0.05 ng/mL) into RUPP rats on GD14 and examined mean arterial pressure (MAP), renal, placental and endothelial cell mt function compared to control RUPP. MAP was elevated in RUPP rats (n = 6) compared to controls (n = 5) (122 ± 5 vs. 102 ± 3 mmHg, p < 0.05), but was reduced by administration of LD recombinant IL-2 (107 ± 1 vs. 122 ± 5 mmHg, n = 9, p < 0.05). Renal, placental and endothelial mt ROS were significantly increased in RUPP rats compared to RUPP+ IL-2 and controls. Placental and renal respiration rates were reduced in RUPP rats compared to control rats but were normalized with IL-2 administration to RUPPs. These data indicate that low-dose IL-2 normalized multi-organ mt function and hypertension in response to placental ischemia.

CD8(+) T cells primed in the absence of CD4(+) T cell help are programmed to produce TRAIL, which results in Death receptor (DR5) mediated apoptosis upon restimulation. Here, we studied whether these 'helpless' effector CD8(+) T cells are consigned to an apoptotic fate or whether their helpless program can be altered by inflammatory or growth cytokines. We found that helpless CD8(+) T cells regained their full proliferative and functional capacity only when IL-2 was added to cell cultures, while IL-7 and IL-15, two common gamma chain cytokines associated with CD8(+) T cell homeostasis and memory, could only partly restore secondary expansion in helpless CD8(+) T cells. Recovery of functional CD8(+) T cell immunity by IL-2 was concomitant with induction of IL2Rα (CD25) expression, downregulation of TRAIL, and the upregulation of anti-apoptotic molecules Bcl-2 and FLIP. The addition of IL-2 to helpless CD8(+) T cells also interfered with DR5-mediated apoptosis induction, indicating that IL-2 affects several components of the TRAIL-DR5 pathway. Collectively, these data demonstrate that the helpless phenotype is not fixed, and that IL-2R signaling at the time of reactivation can play an important role in restoring CD8(+) T cell function.